Structure of PDB 3k5m Chain A Binding Site BS03

Receptor Information
>3k5m Chain A (length=768) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PHMAQAGFILTRHWRDTPQGTEVSFWLATDNGPLQVTLAPQESVAFIPAD
QVPRAQHILQGEQGFRLTPLALKDFHRQPVYGLYCRAHRQLMNYEKRLRE
GGVTVYEADVRPPERYLMERFITSPVWVEGDMHNGTIVNARLKPHPDYRP
PLKWVSIDIETTRHGELYCIGLEGCGQRIVYMLGPENGDASSLDFELEYV
ASRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGR
DNSELEWREHKNGFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELL
GEGSIDNPWDRMDEIDRRFAEDKPALATYNLKNCELVTQIFHKTEIMPFL
LERATVNGLPVDRHGGSVAAFGHLYFPRMHRAGYVAPNLGEVPPHASPGG
YVMDSRPGLYDSVLVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHSTE
GFLDAWFSREKHCLPEIVTNIWHGRDEAKRQGNKPLSQALKIIMNAFYGV
LGTTACRFFDPRLASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVW
LKGAHSEEEAAKIGRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFL
MPTIRGADTGSKKRYAGLIQEGDKQRMVFKGLETVRTDWTPLAQQFQQEL
YLRIFRNEPYQEYVRETIDKLMAGELDARLVYRKRLRRPLSEYQRNVPPH
VRAARLADEENQKRGRPLQYQNRGTIKYVWTTNGPEPLDYQRSPLDYEHY
LTRQLQPVAEGILPFIED
Ligand information
Ligand IDDG3
InChIInChI=1S/C10H16N5O12P3/c11-10-13-8-7(9(16)14-10)12-4-15(8)6-2-1-5(25-6)3-24-29(20,21)27-30(22,23)26-28(17,18)19/h4-6H,1-3H2,(H,20,21)(H,22,23)(H2,17,18,19)(H3,11,13,14,16)/t5-,6+/m0/s1
InChIKeyHDRRAMINWIWTNU-NTSWFWBYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@H]3CC[C@@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3CC[C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3CC[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc2c(n1C3CCC(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N=C(NC2=O)N
FormulaC10 H16 N5 O12 P3
Name2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL54224
DrugBank
ZINCZINC000013516810
PDB chain3k5m Chain A Residue 914 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3k5m Structural insight into translesion synthesis by DNA Pol II.
Resolution2.04 Å
Binding residue
(original residue number in PDB)		S422 R477 K493 N497 Y500 D547
Binding residue
(residue number reindexed from 1)		S420 R475 K491 N495 Y498 D545
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0008296 3'-5'-DNA exonuclease activity
Biological Process
GO:0006261 DNA-templated DNA replication
GO:0006281 DNA repair
GO:0006974 DNA damage response
GO:0009432 SOS response
GO:0045004 DNA replication proofreading
GO:0071897 DNA biosynthetic process

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3k5m, PDBe:3k5m, PDBj:3k5m
PDBsum3k5m
PubMed20064374
UniProtP21189|DPO2_ECOLI DNA polymerase II (Gene Name=polB)

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