Structure of PDB 4xg1 Chain B Binding Site BS04

Receptor Information
>4xg1 Chain B (length=418) Species: 357804 (Psychromonas ingrahamii 37) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DHFNYQNDGRLFVEGLPVEQVVKKTGTPAYIYSRATIERHWQAFDSAAGK
HPHLICYAVKANSNLAVLNLMARMGSGFDIVSVGELMRVIQAGGDPKKIV
FSGVGKTEIEISAALQANIMCFNVESISELYRINSVAKALNVKAPISIRI
NPNIDAGTHPYISTGLKENKFGIEIEQALDVYKIASDLEFLEIKGVDCHI
GSQLTEIAPFIEALDKLLILIDLLAEKGITISHLDLGGGLGVPYDDETPP
EPAEYMTAIINRMAGRSLKLIFEPGRAIMANAGVLVTKVEFLKLNKNFAI
VDAAMNDLIRPALYSAWQNIIPLNTDYQDGQDRPVRSYDIVGPICETGDF
LGKERQLALAEGDYLVIRSTGAYGSTMSSNYNSRCRAAEILVDGEKAFIV
REREELKDLWRGEHILPI
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 B Residue 508 [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]
PDB4xg1 Expression to crystallization of diaminopimelate decarboxylase from the psychrophile Psychromonas ingrahamii
Resolution2.5 Å
Binding residue
(original residue number in PDB)
K61 D80 H200 S203 G240 E274 G276 R277 R313 Y317 Y376
Binding residue
(residue number reindexed from 1)
K60 D79 H199 S202 G239 E273 G275 R276 R310 Y314 Y373
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K61 H200 E274
Catalytic site (residue number reindexed from 1) K60 H199 E273
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

View graph for
Molecular Function

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

[Back to BioLiP]