Structure of PDB 3pml Chain B Binding Site BS05

Receptor Information
>3pml Chain B (length=324) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSY
QEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGT
KTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIE
QTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSR
LLDSLRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFAC
ALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVL
PTPTEKDVFRLLGLPYREPAERDW
Ligand information
Ligand ID1GC
InChIInChI=1S/C11H18N5O12P3/c12-11-14-9-8(10(18)15-11)13-3-16(9)7-1-5(17)6(27-7)2-26-29(19,20)4-30(21,22)28-31(23,24)25/h3,5-7,17H,1-2,4H2,(H,19,20)(H,21,22)(H2,23,24,25)(H3,12,14,15,18)/t5-,6+,7+/m0/s1
InChIKeyJTBKCZGNQPBEJY-RRKCRQDMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc2c(n1C3CC(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.7.0c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)O3
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)O3
FormulaC11 H18 N5 O12 P3
Name2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine
ChEMBLCHEMBL1162300
DrugBank
ZINCZINC000040953629
PDB chain3pml Chain B Residue 702 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3pml Replication infidelity via a mismatch with Watson-Crick geometry.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		R386 G416 S417 D427 D429 Y505 F506 T507 G508 N513
Binding residue
(residue number reindexed from 1)		R140 G170 S171 D181 D183 Y254 F255 T256 G257 N262
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D427 D429 D490
Catalytic site (residue number reindexed from 1) D181 D183 D239
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
4.2.99.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0016779 nucleotidyltransferase activity
GO:0034061 DNA polymerase activity
Biological Process
GO:0006281 DNA repair

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Molecular Function
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Biological Process
External links
PDB RCSB:3pml, PDBe:3pml, PDBj:3pml
PDBsum3pml
PubMed21233421
UniProtQ9UGP5|DPOLL_HUMAN DNA polymerase lambda (Gene Name=POLL)

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