Structure of PDB 4xg1 Chain D Binding Site BS01

Receptor Information
>4xg1 Chain D (length=403) Species: 357804 (Psychromonas ingrahamii 37) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DHFNYQNDGRLFVEGLPVEQVVKKTGTPAYIYSRATIERHWQAFDSAAGH
PHLICYAVKANSNLAVLNLMARMGSGFDIVSVGELMRVIQAGGDPKKIVF
SGVGKTEIEISAALQANIMCFNVESISELYRINSVAKALNVKAPISIRIN
PENKFGIEIEQALDVYKIASDLEFLEIKGVDCHIGSQLTEIAPFIEALDK
LLILIDLLAEKITISHLDLGGGLGVPYDDETPPEPAEYMTAIINRMGRSL
KLIFEPGRAIMANAGVLVTKVEFLKLNDKNFAIVDAAMNDLIRPALYSAW
QNIIPLNTDYQDGQDRPVRSYDIVGPICETGDFLGKERQLALAEGDYLVI
RSTGAYGSTMSSNYNSRCRAAEILVDGEKAFIVREREELKDLWRGEHILP
IHH
Ligand information
Ligand IDLLP
InChIInChI=1S/C14H22N3O7P/c1-9-13(18)11(10(6-17-9)8-24-25(21,22)23)7-16-5-3-2-4-12(15)14(19)20/h6-7,12,18H,2-5,8,15H2,1H3,(H,19,20)(H2,21,22,23)/b16-7+/t12-/m0/s1
InChIKeyYQSOQJORMNSDJL-QFULYMJESA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ncc(CO[P](O)(O)=O)c(C=NCCCC[CH](N)C(O)=O)c1O
ACDLabs 12.01n1c(C)c(O)c(\C=N\CCCCC(N)C(=O)O)c(c1)COP(=O)(O)O
OpenEye OEToolkits 1.7.6Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/CCCCC(C(=O)O)N)O
CACTVS 3.385Cc1ncc(CO[P](O)(O)=O)c(C=NCCCC[C@H](N)C(O)=O)c1O
OpenEye OEToolkits 1.7.6Cc1c(c(c(cn1)COP(=O)(O)O)C=NCCCCC(C(=O)O)N)O
FormulaC14 H22 N3 O7 P
Name(2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid;
N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE
ChEMBL
DrugBankDB04083
ZINCZINC000034150380
PDB chain4xg1 Chain C Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4xg1 Expression to crystallization of diaminopimelate decarboxylase from the psychrophile Psychromonas ingrahamii
Resolution2.5 Å
Binding residue
(original residue number in PDB)
C348 E349
Binding residue
(residue number reindexed from 1)
C328 E329
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K61 H200 E274
Catalytic site (residue number reindexed from 1) K59 H183 E255
Enzyme Commision number 4.1.1.20: diaminopimelate decarboxylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008836 diaminopimelate decarboxylase activity
GO:0016830 carbon-carbon lyase activity
GO:0016831 carboxy-lyase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate

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Molecular Function

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Biological Process
External links
PDB RCSB:4xg1, PDBe:4xg1, PDBj:4xg1
PDBsum4xg1
PubMed
UniProtA1SR00

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