Structure of PDB 2cfm Chain A Binding Site BS01

Receptor Information
>2cfm Chain A (length=561) Species: 2261 (Pyrococcus furiosus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRYLELAQLYQKLEKTTMKLIKTRLVADFLKKVPDDHLEFIPYLILGEVF
PEWDERELGVGEKLLIKAVAMATGIDAKEIEESVKDTGDLGESIALAVKK
KKQKSFFSQPLTIKRVYQTLVKVAETTGEGSQDKKVKYLADLFMDAEPLE
AKYLARTILGTMRTGVAEGLLRDAIAMAFHVKVELVERAYMLTSDFGYVA
KIAKLEGNEGLAKVQVQLGKPIKPMLAQQAASIRDALLEMGGEAEFEIKY
DGARVQVHKDGSKIIVYSRRLENVTRAIPEIVEALKEAIIPEKAIVEGEL
VAIGENGRPLPFQYVLRRFRRKHNIEEMMEKIPLELNLFDVLYVDGQSLI
DTKFIDRRRTLEEIIKQNEKIKVAENLITKKVEEAEAFYKRALEMGHEGL
MAKRLDAVYEPGNRGKKWLKIKPTMENLDLVIIGAEWGEGRRAHLFGSFI
LGAYDPETGEFLEVGKVGSGFTDDDLVEFTKMLKPLIIKEEGKRVWLQPK
VVIEVTYQEIQKSPKYRSGFALRFPRFVALRDDKGPEDADTIERIAQLYE
LQEKMKGKVES
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 chain2cfm Chain A Residue 1563 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2cfm The Closed Structure of an Archaeal DNA Ligase from Pyrococcus Furiosus.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		L226 A227 E247 K249 Y250 R254 R269 E299 F339 M401 K403 K420
Binding residue
(residue number reindexed from 1)		L226 A227 E247 K249 Y250 R254 R269 E299 F339 M401 K403 K420
Annotation score4
Enzymatic activity
Enzyme Commision number 6.5.1.1: DNA ligase (ATP).
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003909 DNA ligase activity
GO:0003910 DNA ligase (ATP) activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0006260 DNA replication
GO:0006266 DNA ligation
GO:0006273 lagging strand elongation
GO:0006281 DNA repair
GO:0006310 DNA recombination
GO:0051301 cell division
GO:0071897 DNA biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2cfm, PDBe:2cfm, PDBj:2cfm
PDBsum2cfm
PubMed16820169
UniProtP56709|DNLI_PYRFU DNA ligase (Gene Name=lig)

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