HEADER TRANSFERASE 15-AUG-19 6SKJ TITLE DELTAC2 C-TERMINAL TRUNCATION OF HSNMT1 IN COMPLEX WITH MYRCOA AND TITLE 2 GNCFSKPR SUBSTRATES COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MYRISTOYL-COA:PROTEIN N-MYRISTOYLTRANSFERASE 1,TYPE I N- COMPND 5 MYRISTOYLTRANSFERASE,PEPTIDE N-MYRISTOYLTRANSFERASE 1; COMPND 6 EC: 2.3.1.97; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: APOPTOSIS-INDUCING FACTOR 3; COMPND 11 CHAIN: C, D; COMPND 12 SYNONYM: APOPTOSIS-INDUCING FACTOR-LIKE PROTEIN; COMPND 13 EC: 1.-.-.-; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES; COMPND 16 OTHER_DETAILS: CONFORMATION A GNCFSKPR AND MYRCOA CONFORMATION B COMPND 17 TETRAHEDRAL INTERMEDIATE (MYB)GNCFSKPR SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NMT1, NMT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2 PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 DERIVATIVE; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS NMT, MYRISTOYLTRANSFERASE TYPE1, ACYLTRANSFERASE, GNAT, GCN5-RELATED KEYWDS 2 N-ACETYLTRANSFERASES, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.DIAN,F.B.RIVIERE,T.ASENSIO,C.GIGLIONE,T.MEINNEL REVDAT 2 24-JAN-24 6SKJ 1 LINK REVDAT 1 18-MAR-20 6SKJ 0 JRNL AUTH C.DIAN,I.PEREZ-DORADO,F.RIVIERE,T.ASENSIO,P.LEGRAND, JRNL AUTH 2 M.RITZEFELD,M.SHEN,E.COTA,T.MEINNEL,E.W.TATE,C.GIGLIONE JRNL TITL HIGH-RESOLUTION SNAPSHOTS OF HUMAN N-MYRISTOYLTRANSFERASE IN JRNL TITL 2 ACTION ILLUMINATE A MECHANISM PROMOTING N-TERMINAL LYS AND JRNL TITL 3 GLY MYRISTOYLATION. JRNL REF NAT COMMUN V. 11 1132 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32111831 JRNL DOI 10.1038/S41467-020-14847-3 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.8 REMARK 3 NUMBER OF REFLECTIONS : 18321 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.340 REMARK 3 FREE R VALUE TEST SET COUNT : 978 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 49.3710 - 5.3543 1.00 2861 181 0.1838 0.1858 REMARK 3 2 5.3543 - 4.2506 1.00 2779 158 0.1486 0.1643 REMARK 3 3 4.2506 - 3.7135 0.99 2777 162 0.1685 0.2059 REMARK 3 4 3.7135 - 3.3741 0.96 2678 131 0.1976 0.2542 REMARK 3 5 3.3741 - 3.1323 0.89 2500 136 0.2226 0.2491 REMARK 3 6 3.1323 - 2.9476 0.77 2111 126 0.2448 0.2966 REMARK 3 7 2.9476 - 2.8000 0.59 1637 84 0.2720 0.3746 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 6872 REMARK 3 ANGLE : 0.738 9361 REMARK 3 CHIRALITY : 0.051 1017 REMARK 3 PLANARITY : 0.005 1164 REMARK 3 DIHEDRAL : 18.045 4198 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6SKJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1292103849. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978565 REMARK 200 MONOCHROMATOR : SI (111) CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22838 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 49.371 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 1.91800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.6.0 REMARK 200 STARTING MODEL: 5O9V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19% PEG6K, 100MM SODIUM CITRATE PH REMARK 280 5.6, 100MM MGCL2, 100MM NACL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 46.48250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.13500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 46.48250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.13500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 637 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 95 REMARK 465 GLY A 96 REMARK 465 SER A 97 REMARK 465 GLU A 98 REMARK 465 PHE A 99 REMARK 465 SER A 100 REMARK 465 VAL A 101 REMARK 465 GLY A 102 REMARK 465 GLN A 103 REMARK 465 HIS A 410 REMARK 465 PRO A 411 REMARK 465 THR A 412 REMARK 465 HIS A 413 REMARK 465 GLY B 95 REMARK 465 GLY B 96 REMARK 465 SER B 97 REMARK 465 GLU B 98 REMARK 465 PHE B 99 REMARK 465 SER B 100 REMARK 465 VAL B 101 REMARK 465 GLY B 102 REMARK 465 GLN B 103 REMARK 465 GLY B 104 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 114 CG CD CE NZ REMARK 470 GLN A 154 CG CD OE1 NE2 REMARK 470 ARG A 166 NE CZ NH1 NH2 REMARK 470 LYS A 170 CG CD CE NZ REMARK 470 LYS A 253 CG CD CE NZ REMARK 470 LYS A 305 CE NZ REMARK 470 ARG A 316 CB CG CD NE CZ NH1 NH2 REMARK 470 LYS A 325 CG CD CE NZ REMARK 470 ARG A 328 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 409 CG OD1 ND2 REMARK 470 LYS A 414 CG CD CE NZ REMARK 470 GLU B 110 CG CD OE1 OE2 REMARK 470 GLU B 111 CG CD OE1 OE2 REMARK 470 LYS B 114 CG CD CE NZ REMARK 470 GLN B 154 CG CD OE1 NE2 REMARK 470 ARG B 166 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 170 CG CD CE NZ REMARK 470 ARG B 258 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 304 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 316 CB CG CD NE CZ NH1 NH2 REMARK 470 ASN B 317 CG OD1 ND2 REMARK 470 GLN B 321 CG CD OE1 NE2 REMARK 470 LYS B 325 CG CD CE NZ REMARK 470 LYS B 417 CG CD CE NZ REMARK 470 LYS B 466 CG CD CE NZ REMARK 470 ARG C 9 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 211 72.20 -102.37 REMARK 500 TYR A 236 -105.44 55.04 REMARK 500 ARG A 316 -71.70 -33.89 REMARK 500 ASN A 317 57.62 -109.64 REMARK 500 ILE A 381 -72.48 -135.00 REMARK 500 PHE A 422 -106.51 -112.81 REMARK 500 THR A 427 -37.19 -131.64 REMARK 500 MET A 456 -155.50 56.17 REMARK 500 PRO B 153 171.58 -55.94 REMARK 500 ASP B 159 114.51 -167.51 REMARK 500 TYR B 180 -157.93 -89.45 REMARK 500 HIS B 211 76.42 -105.40 REMARK 500 TYR B 236 -112.56 49.14 REMARK 500 ILE B 381 -67.84 -134.22 REMARK 500 THR B 412 -61.31 -95.50 REMARK 500 PHE B 422 -104.73 -98.08 REMARK 500 GLN B 428 -32.35 -136.87 REMARK 500 MET B 456 -148.27 54.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue COA B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MYA C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MYR D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide MYA D 202 and GLY D REMARK 800 2 DBREF 6SKJ A 99 494 UNP P30419 NMT1_HUMAN 99 494 DBREF 6SKJ B 99 494 UNP P30419 NMT1_HUMAN 99 494 DBREF 6SKJ C 2 9 UNP Q96NN9 AIFM3_HUMAN 2 9 DBREF 6SKJ D 2 9 UNP Q96NN9 AIFM3_HUMAN 2 9 SEQADV 6SKJ GLY A 95 UNP P30419 EXPRESSION TAG SEQADV 6SKJ GLY A 96 UNP P30419 EXPRESSION TAG SEQADV 6SKJ SER A 97 UNP P30419 EXPRESSION TAG SEQADV 6SKJ GLU A 98 UNP P30419 EXPRESSION TAG SEQADV 6SKJ GLY B 95 UNP P30419 EXPRESSION TAG SEQADV 6SKJ GLY B 96 UNP P30419 EXPRESSION TAG SEQADV 6SKJ SER B 97 UNP P30419 EXPRESSION TAG SEQADV 6SKJ GLU B 98 UNP P30419 EXPRESSION TAG SEQADV 6SKJ ASN C 3 UNP Q96NN9 GLY 3 ENGINEERED MUTATION SEQADV 6SKJ ARG C 9 UNP Q96NN9 LYS 9 CONFLICT SEQADV 6SKJ ASN D 3 UNP Q96NN9 GLY 3 ENGINEERED MUTATION SEQADV 6SKJ ARG D 9 UNP Q96NN9 LYS 9 CONFLICT SEQRES 1 A 400 GLY GLY SER GLU PHE SER VAL GLY GLN GLY PRO ALA LYS SEQRES 2 A 400 THR MET GLU GLU ALA SER LYS ARG SER TYR GLN PHE TRP SEQRES 3 A 400 ASP THR GLN PRO VAL PRO LYS LEU GLY GLU VAL VAL ASN SEQRES 4 A 400 THR HIS GLY PRO VAL GLU PRO ASP LYS ASP ASN ILE ARG SEQRES 5 A 400 GLN GLU PRO TYR THR LEU PRO GLN GLY PHE THR TRP ASP SEQRES 6 A 400 ALA LEU ASP LEU GLY ASP ARG GLY VAL LEU LYS GLU LEU SEQRES 7 A 400 TYR THR LEU LEU ASN GLU ASN TYR VAL GLU ASP ASP ASP SEQRES 8 A 400 ASN MET PHE ARG PHE ASP TYR SER PRO GLU PHE LEU LEU SEQRES 9 A 400 TRP ALA LEU ARG PRO PRO GLY TRP LEU PRO GLN TRP HIS SEQRES 10 A 400 CYS GLY VAL ARG VAL VAL SER SER ARG LYS LEU VAL GLY SEQRES 11 A 400 PHE ILE SER ALA ILE PRO ALA ASN ILE HIS ILE TYR ASP SEQRES 12 A 400 THR GLU LYS LYS MET VAL GLU ILE ASN PHE LEU CYS VAL SEQRES 13 A 400 HIS LYS LYS LEU ARG SER LYS ARG VAL ALA PRO VAL LEU SEQRES 14 A 400 ILE ARG GLU ILE THR ARG ARG VAL HIS LEU GLU GLY ILE SEQRES 15 A 400 PHE GLN ALA VAL TYR THR ALA GLY VAL VAL LEU PRO LYS SEQRES 16 A 400 PRO VAL GLY THR CYS ARG TYR TRP HIS ARG SER LEU ASN SEQRES 17 A 400 PRO ARG LYS LEU ILE GLU VAL LYS PHE SER HIS LEU SER SEQRES 18 A 400 ARG ASN MET THR MET GLN ARG THR MET LYS LEU TYR ARG SEQRES 19 A 400 LEU PRO GLU THR PRO LYS THR ALA GLY LEU ARG PRO MET SEQRES 20 A 400 GLU THR LYS ASP ILE PRO VAL VAL HIS GLN LEU LEU THR SEQRES 21 A 400 ARG TYR LEU LYS GLN PHE HIS LEU THR PRO VAL MET SER SEQRES 22 A 400 GLN GLU GLU VAL GLU HIS TRP PHE TYR PRO GLN GLU ASN SEQRES 23 A 400 ILE ILE ASP THR PHE VAL VAL GLU ASN ALA ASN GLY GLU SEQRES 24 A 400 VAL THR ASP PHE LEU SER PHE TYR THR LEU PRO SER THR SEQRES 25 A 400 ILE MET ASN HIS PRO THR HIS LYS SER LEU LYS ALA ALA SEQRES 26 A 400 TYR SER PHE TYR ASN VAL HIS THR GLN THR PRO LEU LEU SEQRES 27 A 400 ASP LEU MET SER ASP ALA LEU VAL LEU ALA LYS MET LYS SEQRES 28 A 400 GLY PHE ASP VAL PHE ASN ALA LEU ASP LEU MET GLU ASN SEQRES 29 A 400 LYS THR PHE LEU GLU LYS LEU LYS PHE GLY ILE GLY ASP SEQRES 30 A 400 GLY ASN LEU GLN TYR TYR LEU TYR ASN TRP LYS CYS PRO SEQRES 31 A 400 SER MET GLY ALA GLU LYS VAL GLY LEU VAL SEQRES 1 B 400 GLY GLY SER GLU PHE SER VAL GLY GLN GLY PRO ALA LYS SEQRES 2 B 400 THR MET GLU GLU ALA SER LYS ARG SER TYR GLN PHE TRP SEQRES 3 B 400 ASP THR GLN PRO VAL PRO LYS LEU GLY GLU VAL VAL ASN SEQRES 4 B 400 THR HIS GLY PRO VAL GLU PRO ASP LYS ASP ASN ILE ARG SEQRES 5 B 400 GLN GLU PRO TYR THR LEU PRO GLN GLY PHE THR TRP ASP SEQRES 6 B 400 ALA LEU ASP LEU GLY ASP ARG GLY VAL LEU LYS GLU LEU SEQRES 7 B 400 TYR THR LEU LEU ASN GLU ASN TYR VAL GLU ASP ASP ASP SEQRES 8 B 400 ASN MET PHE ARG PHE ASP TYR SER PRO GLU PHE LEU LEU SEQRES 9 B 400 TRP ALA LEU ARG PRO PRO GLY TRP LEU PRO GLN TRP HIS SEQRES 10 B 400 CYS GLY VAL ARG VAL VAL SER SER ARG LYS LEU VAL GLY SEQRES 11 B 400 PHE ILE SER ALA ILE PRO ALA ASN ILE HIS ILE TYR ASP SEQRES 12 B 400 THR GLU LYS LYS MET VAL GLU ILE ASN PHE LEU CYS VAL SEQRES 13 B 400 HIS LYS LYS LEU ARG SER LYS ARG VAL ALA PRO VAL LEU SEQRES 14 B 400 ILE ARG GLU ILE THR ARG ARG VAL HIS LEU GLU GLY ILE SEQRES 15 B 400 PHE GLN ALA VAL TYR THR ALA GLY VAL VAL LEU PRO LYS SEQRES 16 B 400 PRO VAL GLY THR CYS ARG TYR TRP HIS ARG SER LEU ASN SEQRES 17 B 400 PRO ARG LYS LEU ILE GLU VAL LYS PHE SER HIS LEU SER SEQRES 18 B 400 ARG ASN MET THR MET GLN ARG THR MET LYS LEU TYR ARG SEQRES 19 B 400 LEU PRO GLU THR PRO LYS THR ALA GLY LEU ARG PRO MET SEQRES 20 B 400 GLU THR LYS ASP ILE PRO VAL VAL HIS GLN LEU LEU THR SEQRES 21 B 400 ARG TYR LEU LYS GLN PHE HIS LEU THR PRO VAL MET SER SEQRES 22 B 400 GLN GLU GLU VAL GLU HIS TRP PHE TYR PRO GLN GLU ASN SEQRES 23 B 400 ILE ILE ASP THR PHE VAL VAL GLU ASN ALA ASN GLY GLU SEQRES 24 B 400 VAL THR ASP PHE LEU SER PHE TYR THR LEU PRO SER THR SEQRES 25 B 400 ILE MET ASN HIS PRO THR HIS LYS SER LEU LYS ALA ALA SEQRES 26 B 400 TYR SER PHE TYR ASN VAL HIS THR GLN THR PRO LEU LEU SEQRES 27 B 400 ASP LEU MET SER ASP ALA LEU VAL LEU ALA LYS MET LYS SEQRES 28 B 400 GLY PHE ASP VAL PHE ASN ALA LEU ASP LEU MET GLU ASN SEQRES 29 B 400 LYS THR PHE LEU GLU LYS LEU LYS PHE GLY ILE GLY ASP SEQRES 30 B 400 GLY ASN LEU GLN TYR TYR LEU TYR ASN TRP LYS CYS PRO SEQRES 31 B 400 SER MET GLY ALA GLU LYS VAL GLY LEU VAL SEQRES 1 C 8 GLY ASN CYS PHE SER LYS PRO ARG SEQRES 1 D 8 GLY ASN CYS PHE SER LYS PRO ARG HET GOL A 501 6 HET GOL B 501 6 HET GOL B 502 6 HET COA B 503 48 HET MG B 504 1 HET MYA C 101 126 HET MYR D 201 15 HET MYA D 202 63 HETNAM GOL GLYCEROL HETNAM COA COENZYME A HETNAM MG MAGNESIUM ION HETNAM MYA TETRADECANOYL-COA HETNAM MYR MYRISTIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN MYA MYRISTOYL-COA FORMUL 5 GOL 3(C3 H8 O3) FORMUL 8 COA C21 H36 N7 O16 P3 S FORMUL 9 MG MG 2+ FORMUL 10 MYA 2(C35 H62 N7 O17 P3 S) FORMUL 11 MYR C14 H28 O2 FORMUL 13 HOH *90(H2 O) HELIX 1 AA1 THR A 108 LYS A 114 1 7 HELIX 2 AA2 PHE A 119 GLN A 123 5 5 HELIX 3 AA3 ASP A 165 TYR A 180 1 16 HELIX 4 AA4 SER A 193 ARG A 202 1 10 HELIX 5 AA5 LEU A 207 GLN A 209 5 3 HELIX 6 AA6 LYS A 252 ARG A 255 5 4 HELIX 7 AA7 VAL A 259 LEU A 273 1 15 HELIX 8 AA8 ASN A 302 VAL A 309 1 8 HELIX 9 AA9 THR A 319 TYR A 327 1 9 HELIX 10 AB1 GLU A 342 LYS A 344 5 3 HELIX 11 AB2 ASP A 345 LEU A 357 1 13 HELIX 12 AB3 LYS A 358 PHE A 360 5 3 HELIX 13 AB4 SER A 367 TYR A 376 1 10 HELIX 14 AB5 PRO A 430 LYS A 445 1 16 HELIX 15 AB6 LEU A 455 PHE A 461 5 7 HELIX 16 AB7 GLY A 487 VAL A 491 5 5 HELIX 17 AB8 THR B 108 ARG B 115 1 8 HELIX 18 AB9 PHE B 119 GLN B 123 5 5 HELIX 19 AC1 ASP B 165 TYR B 180 1 16 HELIX 20 AC2 SER B 193 ARG B 202 1 10 HELIX 21 AC3 LEU B 207 GLN B 209 5 3 HELIX 22 AC4 LYS B 252 ARG B 255 5 4 HELIX 23 AC5 ARG B 258 LEU B 273 1 16 HELIX 24 AC6 ASN B 302 VAL B 309 1 8 HELIX 25 AC7 THR B 319 ARG B 328 1 10 HELIX 26 AC8 GLU B 342 LYS B 344 5 3 HELIX 27 AC9 ASP B 345 LYS B 358 1 14 HELIX 28 AD1 SER B 367 TYR B 376 1 10 HELIX 29 AD2 PRO B 430 LYS B 445 1 16 HELIX 30 AD3 GLU B 457 PHE B 461 5 5 HELIX 31 AD4 LEU B 462 LEU B 465 5 4 HELIX 32 AD5 GLY B 487 VAL B 491 5 5 SHEET 1 AA112 PHE A 156 ALA A 160 0 SHEET 2 AA112 HIS A 211 VAL A 216 -1 O ARG A 215 N THR A 157 SHEET 3 AA112 LEU A 222 ILE A 235 -1 O VAL A 223 N VAL A 214 SHEET 4 AA112 THR A 238 VAL A 250 -1 O MET A 242 N ALA A 231 SHEET 5 AA112 ALA A 279 ALA A 283 1 O VAL A 280 N VAL A 243 SHEET 6 AA112 PHE A 467 TYR A 479 -1 O TYR A 479 N ALA A 279 SHEET 7 AA112 GLY A 292 SER A 300 -1 N CYS A 294 O LEU A 474 SHEET 8 AA112 VAL A 449 LEU A 453 -1 O ALA A 452 N TRP A 297 SHEET 9 AA112 ALA A 418 SER A 421 1 N ALA A 419 O ASN A 451 SHEET 10 AA112 VAL A 394 THR A 402 -1 N TYR A 401 O TYR A 420 SHEET 11 AA112 ILE A 382 GLU A 388 -1 N VAL A 387 O THR A 395 SHEET 12 AA112 LEU A 338 PRO A 340 -1 N ARG A 339 O VAL A 386 SHEET 1 AA2 4 PHE A 156 ALA A 160 0 SHEET 2 AA2 4 HIS A 211 VAL A 216 -1 O ARG A 215 N THR A 157 SHEET 3 AA2 4 LEU A 222 ILE A 235 -1 O VAL A 223 N VAL A 214 SHEET 4 AA2 4 LEU A 362 VAL A 365 -1 O THR A 363 N HIS A 234 SHEET 1 AA3 3 PHE A 188 PHE A 190 0 SHEET 2 AA3 3 SER A 405 ILE A 407 -1 O THR A 406 N ARG A 189 SHEET 3 AA3 3 SER A 415 LEU A 416 -1 O LEU A 416 N SER A 405 SHEET 1 AA411 PHE B 156 ALA B 160 0 SHEET 2 AA411 HIS B 211 VAL B 216 -1 O ARG B 215 N THR B 157 SHEET 3 AA411 LEU B 222 ILE B 235 -1 O VAL B 223 N VAL B 214 SHEET 4 AA411 THR B 238 VAL B 250 -1 O MET B 242 N ALA B 231 SHEET 5 AA411 ALA B 279 ALA B 283 1 O VAL B 280 N VAL B 243 SHEET 6 AA411 PHE B 467 TYR B 479 -1 O TYR B 479 N ALA B 279 SHEET 7 AA411 GLY B 292 SER B 300 -1 N HIS B 298 O GLY B 468 SHEET 8 AA411 VAL B 449 LEU B 453 -1 O ALA B 452 N TRP B 297 SHEET 9 AA411 ALA B 418 SER B 421 1 N ALA B 419 O ASN B 451 SHEET 10 AA411 VAL B 394 THR B 402 -1 N TYR B 401 O TYR B 420 SHEET 11 AA411 LEU B 362 PRO B 364 0 SHEET 1 AA511 LEU B 338 PRO B 340 0 SHEET 2 AA511 ILE B 382 GLU B 388 -1 O VAL B 386 N ARG B 339 SHEET 3 AA511 VAL B 394 THR B 402 -1 O LEU B 398 N PHE B 385 SHEET 4 AA511 ALA B 418 SER B 421 -1 O TYR B 420 N TYR B 401 SHEET 5 AA511 VAL B 449 LEU B 453 1 O ASN B 451 N ALA B 419 SHEET 6 AA511 GLY B 292 SER B 300 -1 N TRP B 297 O ALA B 452 SHEET 7 AA511 PHE B 467 TYR B 479 -1 O GLY B 468 N HIS B 298 SHEET 8 AA511 ALA B 279 ALA B 283 -1 N ALA B 279 O TYR B 479 SHEET 9 AA511 THR B 238 VAL B 250 1 N VAL B 243 O VAL B 280 SHEET 10 AA511 LEU B 222 ILE B 235 -1 N ALA B 231 O MET B 242 SHEET 11 AA511 VAL B 425 HIS B 426 0 SHEET 1 AA6 3 PHE B 188 PHE B 190 0 SHEET 2 AA6 3 SER B 405 ILE B 407 -1 O THR B 406 N ARG B 189 SHEET 3 AA6 3 SER B 415 LEU B 416 -1 O LEU B 416 N SER B 405 LINK N BGLY C 2 C2MBMYA C 101 1555 1555 1.32 LINK N BGLY D 2 C1 BMYR D 201 1555 1555 1.32 LINK N AGLY D 2 C2MAMYA D 202 1555 1555 1.32 LINK MG MG B 504 O HOH B 635 1555 1555 2.49 CISPEP 1 PRO A 288 LYS A 289 0 -5.52 CISPEP 2 PRO B 288 LYS B 289 0 -7.35 SITE 1 AC1 5 LYS A 289 VAL A 291 LEU A 478 TRP A 481 SITE 2 AC1 5 CYS A 483 SITE 1 AC2 7 PRO B 126 LYS B 289 VAL B 291 LEU B 478 SITE 2 AC2 7 TRP B 481 LYS B 482 CYS B 483 SITE 1 AC3 3 GLN B 123 GLU B 139 ARG B 265 SITE 1 AC4 24 TYR B 117 GLN B 118 PHE B 119 TRP B 120 SITE 2 AC4 24 ASN B 179 TYR B 180 VAL B 181 LEU B 248 SITE 3 AC4 24 CYS B 249 VAL B 250 ARG B 255 SER B 256 SITE 4 AC4 24 LYS B 257 ARG B 258 VAL B 259 ALA B 260 SITE 5 AC4 24 PRO B 261 THR B 282 LEU B 287 HOH B 626 SITE 6 AC4 24 GLY D 2 MYR D 201 MYA D 202 HOH D 301 SITE 1 AC5 3 HIS B 426 THR B 429 HOH B 635 SITE 1 AC6 28 ARG A 115 TYR A 117 GLN A 118 PHE A 119 SITE 2 AC6 28 TRP A 120 ASN A 179 TYR A 180 VAL A 181 SITE 3 AC6 28 ILE A 245 PHE A 247 LEU A 248 CYS A 249 SITE 4 AC6 28 VAL A 250 ARG A 255 SER A 256 ARG A 258 SITE 5 AC6 28 VAL A 259 ALA A 260 PRO A 261 ILE A 264 SITE 6 AC6 28 THR A 268 HIS A 272 ALA A 279 TYR A 281 SITE 7 AC6 28 THR A 282 LEU A 287 TYR A 479 GLY C 2 SITE 1 AC7 13 TRP B 120 ILE B 245 ASN B 246 PHE B 247 SITE 2 AC7 13 LEU B 248 THR B 268 ALA B 279 TYR B 281 SITE 3 AC7 13 THR B 282 TYR B 479 COA B 503 GLY D 2 SITE 4 AC7 13 MYA D 202 SITE 1 AC8 31 TYR B 117 GLN B 118 PHE B 119 TRP B 120 SITE 2 AC8 31 ASN B 179 TYR B 180 VAL B 181 ILE B 245 SITE 3 AC8 31 ASN B 246 PHE B 247 LEU B 248 CYS B 249 SITE 4 AC8 31 VAL B 250 ARG B 255 SER B 256 LYS B 257 SITE 5 AC8 31 ARG B 258 VAL B 259 ALA B 260 PRO B 261 SITE 6 AC8 31 THR B 268 ALA B 279 TYR B 281 THR B 282 SITE 7 AC8 31 LEU B 287 TYR B 479 COA B 503 HOH B 626 SITE 8 AC8 31 ASN D 3 MYR D 201 HOH D 301 CRYST1 92.965 58.270 154.132 90.00 90.92 90.00 C 1 2 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.010757 0.000000 0.000172 0.00000 SCALE2 0.000000 0.017161 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006489 0.00000