Structure of PDB 6vef Chain A Binding Site BS01

Receptor Information
>6vef Chain A (length=844) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DTNVKQVKVLQLINAYRFRGHQHANLDPLGLYQQDKVADLDPSFHDLTEA
DFQETFNVGSFASGKETMKLGELLEALKQTYCGPIGAEYMHITSTEEKRW
IQQRIESGRATFNSEEKKRFLSELTAAEGLERYLGAKFPGAKRFSLEGDA
LIPMLKEMIRHAGNSGTREVVLGMAHRGRLNVLVNVLGKKPQDLFDEFAG
KHKEHLGTGDVKYHMGFSSDFQTDGGLVHLALAFNPSHLEIVSPVVIGSV
RARLDRLDEPSSNKVLPITIHGDAAVTGQGVVQETLNMSKARGYEVGGTV
RIVINNQVGFTTSNPLDARSTPYMTDIGKMVQAPIFHVNADDPEAVAFVT
RLALDFRNTFKRDVFIDLVCYRRHGHNEADEPSATQKIKKHPTPRKIYAD
KLEQEKVATLEDATEMVNLYRDALDAGDCVVAEWRPMNMHSFTWSPYLNH
EWDEEYPNKVEMKRLQELAKRISTVPEAVEMQSRVAKIYGDRQAMAAGEK
LFDWGGAENLAYATLVDEGIPVRLSGEDSGRGTFFHRHAVIHNQSNGSTY
TPLQHIHNGQGAFRVWDSVLSEEAVLAFEYGYATAEPRTLTIWEAQFGDF
ANGAQVVIDQFISSGEQKWGRMCGLVMLLPHGYEGQGPEHSSARLERYLQ
LCAEQNMQVCVPSTPAQVYHMLRRQALRGMRRPLVVMSPKSLLRHPLAVS
SLEELANGTFLPAIGEIDELDPKGVKRVVMCSGKVYYDLLEQRRKNNQHD
VAIVRIEQLYPFPHKAMQEVLQQFAHVKDFVWCQEEPLNQGAWYCSQHHF
REVIPFGASLRYAGRPASASPAVGHMSVHQKQQQDLVNDALNVE
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 chain6vef Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6vef Cryo-EM Structure of Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA
Resolution4.08 Å
Binding residue
(original residue number in PDB)		H313 R337 S530 F531 W533 R710 M711
Binding residue
(residue number reindexed from 1)		H229 R253 S441 F442 W444 R621 M622
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:6vef, PDBe:6vef, PDBj:6vef
PDBsum6vef
PubMed
UniProtP0AFG3|ODO1_ECOLI 2-oxoglutarate dehydrogenase E1 component (Gene Name=sucA)

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