triangle PDBeMotif: 4jvf  
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coner
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coner
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Classification protein binding/inhibitor    | release date: Mon, Mar 25, 2013
Title the crystal structure of pde6d in complex with the inhibitor
Authors A.CHANDRA, A.WITTINGHOFER, B.PAPKE, G.TRIOLA, H.WALDMANN, M.HOFFMANN, N.VARTAK, P.BASTIAENS, S.H, S.ISMAIL, Z.GUNTHER
Method X-RAY DIFFRACTION (resolution: 2.40Å)
PDBe Citation   
Small molecules:    search 17X 17X binding statistics 17X
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chain B sequence:
GSMSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQ
KVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
Residue colours:  hydrophilic   hydrophobic   intermediate 
Assembly 1     View the assembly/model: ( JMolViewer Download PDB file RasMol script viewer AstexViewer™@MSD-EBI )
Motif search   chain:    Sequence numbers: 
   Using:   φ/ψ    residues code    secondary structures   
 coordinates of:  Cαs Side-chain
 
      View the fragment: rasmol script JMol viewer
chain B : RETINAL ROD RHODOPSIN-SENSITIVE CGMP 3',5'-CYCLICPHOSPHODIESTERASE SUBUNIT DELTA;
member of: GENE3D:searchG3DSA_2.70.50.40PANTHER:searchPTHR12976PFAM:searchPF05351PIRSF:searchPIRSF037825SUPERFAMILY:searchSSF81296UniProt:searchO43924
JMol viewer RasMol script viewer  17X 201B  ..             *  *           *     *        *     ** **   *                * *                            *  ..           *                 * * 
sec str:  ..hhhhhhhhhhheeeeeeeeee.....eeeee.........eeeeeee.hhhh..eeeeeeeeee...eeeeeeeeeeee..eeeeeeeeeeeee...eeeeeeeeee....hhhhhh..eeeeeeeee..eeeeeeeeeeeee
sequence :  ..KDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEA..MPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
seq num:  ..4         14        24        34        44        54        64        74        84        94        104     ..118       128       138          
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION ..||      |  |        |  | | || | || ||  |        || ||       ^*** |   |       |                | ^***   |  | ..   | |||||       || | ||| |      
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..*|      |  |        |  ^** || | || ||  |        || ||         || |   |       |                |  |     |  | ..   | |||||       || | ||^**      
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..**      |  |        |  | | || | || ||  |        || ||         ^***   |       |                |  |     ^*** ..   | |||||       || | ||         
search RasMol script viewer Motif-ligand binding stats  TYR_PHOSPHO_SITE ..|       |  |        |  | | || | || ||  |        || ||          | |   ********^                |  |          ..   | |||||       || | ||         
search RasMol script viewer Motif-ligand binding stats  MYRISTYL ..*       |  |        |  | | || | || ||  |        || ||          | |                            |  |          ..   | |||||       || | ||         
search RasMol script viewer Motif-ligand binding stats  asxturn ..        |  |        |  | | || | |***|  |        || ||          | |                            |  |          ..   | |||||       || | ||         
search RasMol script viewer Motif-ligand binding stats  betabulge ..        |  |        |  | | ** | ||  |  |        || ||          | |                            |  |          ..   | |||||       || | **         
search RasMol script viewer Motif-ligand binding stats  betabulgeloop ..        |  |        ******    | ||  |  |        || ||          | |                            |  |          ..   | |||||       || |            
search RasMol script viewer Motif-ligand binding stats  betaturn ..        ****           | |    | ||  |  |        ****|          | |                            ****          ..   | ****|       ****            
search RasMol script viewer Motif-ligand binding stats  nest ..        |  |           ***    | ||  |  |         |  |          | |                            |  |          ..   |  |***        | |            
search RasMol script viewer Motif-ligand binding stats  niche ..        ****           | |    **********         ****          ***                            ****          ..   *******        ***            
search RasMol script viewer Motif-ligand binding stats  stturn ..                       ***                                                                                  ..                                 

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