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BioLiP

Structure of PDB 1dgs Chain A Binding Site BS02

Receptor Information
>1dgs Chain A (length=581) Species: 276 (Thermus filiformis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEER
FPEFKSPDSPTEQVGARPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEER
LEREAEAPSLYTVEHKVDGLSVLYYEEGVWSTGSGDGEVGEEVTQNLLTI
PTIPRRLKGVPDRLEVRGEVYMPIEAFLRLNEELEERGEKVFKNPRNAAA
GSLRQKDPRVTAKRGLRATFYALGLGLGLEESGLKSQYELLLWLKEKGFP
VEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGELGY
TARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSE
VSRVTLHNESYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGKERPI
RWPEACPECGHRLVKEGKVHRCPNPLCPAKRFEAIRHYASRKAMDIEGLG
EKLIERLLEKGLVRDVADLYHLRKEDLLGLERMGEKSAQNLLRQIEESKH
RGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEASLEELIEVEEVGEL
TARAILETLKDPAFRDLVRRLKEAGVSMESK
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 chain1dgs Chain A Residue 700 [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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PDB1dgs Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		E114 K116 E169 Y221 H253 K288 K312
Binding residue
(residue number reindexed from 1)		E114 K116 E169 Y221 H253 K288 K312
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) E114 K116 D118 Y221 K312 C406 C409 C422 C427
Catalytic site (residue number reindexed from 1) E114 K116 D118 Y221 K312 C406 C409 C422 C427
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

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Molecular Function
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Biological Process
External links
PDB RCSB:1dgs, PDBe:1dgs, PDBj:1dgs
PDBsum1dgs
PubMed10698952
UniProtQ9ZHI0|DNLJ_THEFI DNA ligase (Gene Name=ligA)

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