Structure of PDB 4d05 Chain B Binding Site BS01

Receptor Information
>4d05 Chain B (length=249) Species: 1365007 (Psychromonas sp. SP041) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IQLATNYRQDIDVTQYYVSEKLDGIRAYWNGHQLISKQGNIFTAPTWFIA
SFPTTAMDGELWIARQQFETVSGIARTQDNQNEQWKQIKFMIFDLPKSTV
SFEQRINKMQTLVTDTNSPYLQMIEQQKIPNTVALFDLLNKVVMGKGEGL
MLHHQDALYQTSRDLMKLKKFEDAEATVIAYLPGKGKYEGLLGAILVKNE
EGVTFKIGSGFSDEERSTPPPIGSLITYRFTGKTNNNIPRFASFVRIRV
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 chain4d05 Chain B Residue 1260 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4d05 Enzyme-Adenylate Structure of a Bacterial ATP-Dependent DNA Ligase with a Minimized DNA-Binding Surface
Resolution1.65 Å
Binding residue
(original residue number in PDB)		S23 K25 L26 R30 E64 F97 I128 K173
Binding residue
(residue number reindexed from 1)		S19 K21 L22 R26 E60 F93 I124 K167
Annotation score4
Enzymatic activity
Enzyme Commision number 6.5.1.1: DNA ligase (ATP).
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003910 DNA ligase (ATP) activity
GO:0005524 ATP binding
Biological Process
GO:0006260 DNA replication
GO:0006281 DNA repair
GO:0006310 DNA recombination

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4d05, PDBe:4d05, PDBj:4d05
PDBsum4d05
PubMed25372693
UniProtA0A0A6YVN6

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