Structure of PDB 2jgd Chain A Binding Site BS01

Receptor Information
>2jgd Chain A (length=812) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DTNVKQVKVLQLINAYRFRGHQHANLDPLGLWQQDDLDPSFHDLTEDFQE
TFNVGSFAETMKLGELLEALKQTYCGPIGAEYMHITSTEEKRWIQQRIES
RATFNSEEKKRFLSELTAAEGLERYLGAKFPGRFSLEGGDALIPMLKEMI
RHAGNSGTREVVLGMAHRGRLNVLVNVLGKKPQDLFDEFAGKHHLGTGDV
KYHMGFSSDFQTDGGLVHLALAFNPSHLEIVSPVVIGSVRARLDRLDEPS
SNKVLPITIHGDAAVTGQGVVQETLNMSKARGYEVGGTVRIVINNQYCTD
IGKMVQAPIFHVNADDPEAVAFVTRLALDFRNTFKRDVFIDLVCYRRHQP
LMYQKIKKHPTPRKIYADKLEQEKVATLEDATEMVNLYRDALDAGDCVVA
EWRPMNMHSFTWSPYLNHEWDEEYPNKVEMKRLQELAKRISTVPEAVEMQ
SRVAKIYGDRQAMAAGEKLFDWGGAENLAYATLVDEGIPVRLSGEDSGRG
TFFHRHAVIHNQSNGSTYTPLQHIHNGQGAFRVWDSVLSEEAVLAFEYGY
ATAEPRTLTIWEAQFGDFANGAQVVIDQFISSGEQKWGRMCGLVMLLPHG
YEGQGPEHSSARLERYLQLCAEQNMQVCVPSTPAQVYHMLRRQALRGMRR
PLVVMSPKSLLRHPLAVSSLEELANGTFLPAIGEIDELDPKGVKRVVMCS
GKVYYDLLEQRRKNNQHDVAIVRIEQLYPFPHKAMQEVLQQFAHVKDFVW
CQEEPLNQGAWYCSQHHFREVIPFGASLRYAGRPASASPAVGHMSVHQKQ
QQDLVNDALNVE
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 chain2jgd Chain A Residue 1934 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2jgd Crystal Structure of the E1 Component of the Escherichia Coli 2-Oxoglutarate Dehydrogenase Multienzyme Complex.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		S302 H313 R337 M526 W533 T673 R710 M711
Binding residue
(residue number reindexed from 1)		S207 H218 R242 M405 W412 T552 R589 M590
Annotation score1
Enzymatic activity
Enzyme Commision number 1.2.4.2: oxoglutarate dehydrogenase (succinyl-transferring).
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
GO:0030976 thiamine pyrophosphate binding
GO:0042802 identical protein binding
Biological Process
GO:0006099 tricarboxylic acid cycle
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0045252 oxoglutarate dehydrogenase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2jgd, PDBe:2jgd, PDBj:2jgd
PDBsum2jgd
PubMed17367808
UniProtP0AFG3|ODO1_ECOLI 2-oxoglutarate dehydrogenase E1 component (Gene Name=sucA)

[Back to BioLiP]