triangle PDBeMotif: 3lzi  
  coner Sequences coner   coner 3D motifs coner   coner Ligand environment coner   coner Ligand bonds coner
   
coner
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coner
AstexViewer TM
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Enzyme   2.7.7.7
Classification transferase/dna    | release date: Mon, Mar 1, 2010
Title rb69 dna polymerase (y567a) ternary complex with datp opposi dihydro-8-oxoguanine
Authors G.BLAHA, J.BECKMAN, J.WANG, M.WANG, W.H.KONIGSBERG
Method X-RAY DIFFRACTION (resolution: 2.30Å)
PDBe Citation   
Small molecules:    search CA CA binding statistics CA   search DTP DTP binding statistics DTP
Modified residues:  search 8OG 8OG binding statistics 8OG search DOC DOC binding statistics DOC
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chain A sequence:
MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGL
EALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVE
EWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAK
RLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRY
ISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPI
PNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFN
QRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRK
LLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESK
FRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRY
AEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPK
CPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPL
EGFTSAAKLDYEKKASLFDMFDF
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 A : DNA POLYMERASE
member of: CATH:search3.30.342.10/search3.30.420.10/search3.40.1820.10GENE3D:searchG3DSA_1.10.287.690/searchG3DSA_3.30.342.10/searchG3DSA_3.30.420.10/searchG3DSA_3.90.1600.10PANTHER:searchPTHR10322PFAM:searchPF00136/searchPF03104PRINTS:searchDNAPOLBPROSITE PATTERNS:searchPS00116, SMART:searchSM00486SUPERFAMILY:searchSSF53098/searchSSF56672UniProt:searchQ38087
JMol viewer RasMol script viewer  CA 909A  ..                                                                                                                   *                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
JMol viewer RasMol script viewer  CA 908A  ..                                                                                                                   |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       *                                                                                                                                                                                           
JMol viewer RasMol script viewer  CA 907A  ..                                                                                                                   |                                                                                                                                                                                                                                                                                                      *                                                                                                                                                                                                                   *                                                                                            |                                                                                                                                                                                           
JMol viewer RasMol script viewer  CA 906A  ..                                                                                                                   |                                                                                                                                                                                                                                                                                                      |                                                                                             * *                       *                                                                                           |                                                                                            |                                                                                                                                                                                           
JMol viewer RasMol script viewer  CA 905A  ..                                                                                                                   |                                                                                                                                                                                                                                                                                                      **                                                                                            | |                       |                                                                                           *                                                                                            |                                                                                                                                                                                           
JMol viewer RasMol script viewer  DTP 904A  ..                                                                                                                   |                                                                                                                                                                                                                                                                                                      ** ***                                                                 *                      | |                       |                            *   *                                                          *                                                                                            |                                                                                                                                                                                           
sec str:  .....eeeeeee....eeeeee.....eeeeee....eeeee.........ee.....eeeee..hhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhh.eeeeeee..................eeeeee....eeeeeee.ee..ee....hhhhhhhhhhhh....hhhhhh.eeeeee.hhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhhh....eeee..........eeee...ee.hhhhhhhhhh.......hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.ee......................ee...eeeeee.hhhhhhhhhhh.....eeee....hhhhhhh..........ee....eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee..eeeeehhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee..........eeeee..eeeeeeeee..eeeeeeeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee..hhhhhh.........hhhhhhhhhhhhhh.............eeeeee..........eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh...
sequence :  ..MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFDF
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891          
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION ..             |  |     | | |     |            ||||   | |  | |   |   |         | |    | |    |   |        |  |         |  |      ||||     |  || |||        | |||    |  || ||| |||| |   || ||      |   |       |   |       | |                  | |||| |||   |     |       |  ||  | |  || || |   | |   ||  || |       |  |   |                      ||||^***     | |   |  |   |       | |||||                                   | | |    ||| | ||  | |     || ||||   | ||  | |||       |  | | |                              ^*** |    |  |  |   |  || || ||  |   |   | |   |      |   |  || ||| |  ||||^***  |                    | |  || | | | |   |                                     |     ||||||                  | | |   |||||         |    |    |  |||||  | |                   |  |        |  |  |  |      | |  |     |  |           |  | |  |   |  |       | || | |     |||||  |      |  || | |   |    ||  || | |   | || ||    
search RasMol script viewer Motif-ligand binding stats  CAMP_PHOSPHO_SITE ..             |  |     | | |     |            ||||   | |  | |   |   |         | |    | |    |   |        |  |         |  |      ||||     |  || |||        | |||    |  || ||| |||| |   || ||      |   |       |   |       | |                  | **^* |||   |     |       |  ||  | |  |**^* |   | |   ||  || |       |  |   |                      ||||         | |   |  |   |       | |||||                                   | | |    ||| | ||  | |     || ||||   | ||  | |||       |  | | |                                |  |    |  |  |   |  |**^* ||  |   |   | |   |      |   |  || ||| |  ||||  |   |                    | |  || | | | |   |                                     |     ||||||                  | | |   |||||         |    |    |  |||||  | |                   |  |        |  |  |  |      | |  |     |  |           |  | |  |   |  |       | || | |     |||||  |      |  || | |   |    ||  || | |   **^* ||    
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  AMIDATION ..                      | |                    ||||   | |        |   |         | |    | |    |   |        |  |                   ||||           | |        | |||    |  || ||| |||| |   || ||      |   |       |   |       | |                  | || | |||                 |  |   | |  |   | |   | |   |    | |       |  |   |                      ||||         | |   |  |   |         | |||                                   | | |    ||| | ||          || ||||   | ||  | |||          |   |                                        |  |  |   |  |  |          |   | |   |      |   |  || ||  |  ||||  |   |                    | |  || | | | |   |                                           || |||                  | |     ^***|                   |  || ||  |                                 |  |  |  |      | |  |     |  |           |  | |  |   |  |       |  | | |     |  |          |  || | |   |    ||  || | |      | |     
search RasMol script viewer Motif-ligand binding stats  DNA_POLYMERASE_B ..                      | |                    ||||   | |        |   |         | |    | |    |   |        |  |                   ||||           | |        | |||    |  || ||| |||| |   || ||      |   |       |   |       | |                  | || | |||                 |  |   | |  |   | |   | |   |    | |       |  |   |                      ||||         | |   |  |   |         | |||                                   | | |    ||| | ||          || ||||   | ||  | |||          |   |                                        |  |  |   |  |  |          |   | |   |      |   |  || ||  |  ||||  |   |                    | |  || | *********                                           || |||                  | |      |  |                   |  || ||  |                                 |  |  |  |      | |  |     |  |           |  | |  |   |  |       |  | | |     |  |          |  || | |   |    ||  || | |      | |     
search RasMol script viewer Motif-ligand binding stats  asxmotif ..                      | |                    ||||   | |        *****         | |    | |    |   |        |  |                   ||||           | |        | |||    |  || ||| |||| |   || ||      *****       |   |       | |                  | || | |||                 |  |   | |  |   | |   | |   |    | |       |  |   |                      ||||         | |   |  |   |         | |||                                   | | |    ||| | ||          || ||||   | ||  | |||          |   |                                        |  |  |   |  |  |          |   | |   |      |   |  || ||  |  ||||  |   |                    | |  || |   | |                                               || |||                  | |      |  |                   |  || ||  |                                 |  |  |  |      | |  |     |  |           |  | |  |   |  |       |  | | |     |  |          |  || | |   |    ||  || | |      | |     
search RasMol script viewer Motif-ligand binding stats  asxturn ..                      | |                    ||||   | |                      | |    | |    |   |        |  |                   ||||           | |        | |||    |  || ||| |||| |   || ||                  |   |       | |                  | || | |||                 |  |   ***  |   | |   | |   |    | |       |  |   |                      ||||         | |   |  |   |         | |||                                   | | |    ||| | ||          || ||||   | ||  | |||          |   |                                        |  |  |   |  |  |          |   | |   |      |   |  || ||  |  |***  |   |                    | |  || |   | |                                               || |||                  | |      |  |                   |  || ||  |                                 |  |  |  |      | |  |     |  |           |  | |  |   |  |       |  | | |     |  |          |  |*** |   |    ||  || | |      | |     
search RasMol script viewer Motif-ligand binding stats  betabulgeloop ..                      | |                    ||||   | |                      | |    | |    |   |        |  |                   ||||           | |        | |||    |  || ||| |||| |   || ||                  |   |       | |                  | || | |||                 |  |        |   | |   | |   |    | |       |  |   |                      ||||         | |   |  |   |         | |||                                   | | |    ||| | ||          || ||||   | ||  *****          |   |                                        |  |  |   |  |  |          |   | |   |      |   |  || ||  |  | |   |   |                    | |  || |   | |                                               || |||                  | |      |  |                   |  || ||  |                                 |  |  |  |      | |  |     |  |           |  | |  |   |  |       |  | | |     |  |          |  |    |   |    ||  || | |      | |     
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chain T : DNA (5'-D(P*TP*CP*AP*(8OG)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3');
JMol viewer RasMol script viewer  DTP 904A  ..   **             
sec str:  ....................
sequence :  ..TCAGGTAAGCAGTCCGCG
seq num:  ..1         11      

chain P : DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(D
JMol viewer RasMol script viewer  CA 907A  ..             
JMol viewer RasMol script viewer  DTP 904A  ..            *
sec str:  ...............
sequence :  ..GCGGACTGCTTAC
seq num:  ..103          

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