Structure of PDB 1v9p Chain B Binding Site BS02

Receptor Information
>1v9p Chain B (length=584) Species: 276 (Thermus filiformis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEER
FPEFKSPDSPTEQVGARPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEER
LERALGRKRPFLYTVEHKVDGLSVNLYYEEGVLVFGATRGDGEVGEEVTQ
NLLTIPTIPRRLKGVPDRLEVRGEVYMPIEAFLRLNEELEERGEKVFKNP
RNAAAGSLRQKDPRVTAKRGLRATFYALGLGLEESGLKSQYELLLWLKEK
GFPVEHGYEKALGAEGVEEVYRRFLAQRHALPFEADGVVVKLDDLALWRE
LGYTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIE
GSEVSRVTLHNESYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGEE
RPIRWPETCPECGHRLVKEGKVHRCPNPLCPAKRFEAIRHYASRKAMDIE
GLGEKLIERLLEKGLVRDVADLYHLRKEDLLGLERMGEKSAQNLLRQIEE
SKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEASLEELLEVEEV
GELTARAILETLKDPAFRDLVRRLKEAGVSMESK
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain1v9p Chain B Residue 2700 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1v9p Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		E2116 K2118 V2119 E2174 Y2226 K2315
Binding residue
(residue number reindexed from 1)		E116 K118 V119 E174 Y226 K315
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) E2116 K2118 D2120 Y2226 K2315 C2409 C2412 C2425 C2430
Catalytic site (residue number reindexed from 1) E116 K118 D120 Y226 K315 C409 C412 C425 C430
Enzyme Commision number 6.5.1.2: DNA ligase (NAD(+)).
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003911 DNA ligase (NAD+) activity
Biological Process
GO:0006260 DNA replication
GO:0006281 DNA repair

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:1v9p, PDBe:1v9p, PDBj:1v9p
PDBsum1v9p
PubMed10698952
UniProtQ9ZHI0|DNLJ_THEFI DNA ligase (Gene Name=ligA)

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