Structure of PDB 5vo3 Chain A Binding Site BS02

Receptor Information
>5vo3 Chain A (length=380) Species: 727 (Haemophilus influenzae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASNAMKEKVVSLAQDLIRRPSISPNDEGCQQIIAERLEKLGFQIEWMPFN
DTLNLWAKHGTSEPVIAFAGHTDVVPTGDENQWSSPPFSAEIIDGMLYGR
GAADMKGSLAAMIVAAEEYVKANPNHKGTIALLITSDEEATAKDGTIHVV
ETLMARDEKITYCMVGEPSSAKNLGDVVKNGRRGSITGNLYIQGIQGHVA
YPHLAENPIHKAALFLQELTTYQWDKGNEFFPPTSLQIANIHAGTGSNNV
IPAELYIQFNLRYCTEVTDEIIKQKVAEMLEKHNLKYRIEWNLSGKPFLT
KPGKLLDSITSAIEETIGITPKAETGGGTSDGRFIALMGAEVVEFGPLNS
TIHKVNECVSVEDLGKCGEIYHKMLVNLLD
Ligand information
Ligand IDAPI
InChIInChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5+
InChIKeyGMKMEZVLHJARHF-SYDPRGILSA-N
SMILES
SoftwareSMILES
CACTVS 3.370N[CH](CCC[CH](N)C(O)=O)C(O)=O
OpenEye OEToolkits 1.7.2C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N
OpenEye OEToolkits 1.7.2C(CC(C(=O)O)N)CC(C(=O)O)N
CACTVS 3.370N[C@@H](CCC[C@@H](N)C(O)=O)C(O)=O
ACDLabs 12.01O=C(O)C(N)CCCC(C(=O)O)N
FormulaC7 H14 N2 O4
Name2,6-DIAMINOPIMELIC ACID
ChEMBLCHEMBL415306
DrugBank
ZINCZINC000001532722
PDB chain5vo3 Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vo3 Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism.
Resolution1.954 Å
Binding residue
(original residue number in PDB)		E134 E135 A136 S181 R258 S290 G324 T325
Binding residue
(residue number reindexed from 1)		E138 E139 A140 S185 R262 S294 G328 T329
Annotation score5
Enzymatic activity
Enzyme Commision number 3.5.1.18: succinyl-diaminopimelate desuccinylase.
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding
GO:0009014 succinyl-diaminopimelate desuccinylase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0050897 cobalt ion binding
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5vo3, PDBe:5vo3, PDBj:5vo3
PDBsum5vo3
PubMed29272107
UniProtP44514|DAPE_HAEIN Succinyl-diaminopimelate desuccinylase (Gene Name=dapE)

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