Structure of PDB 4fir Chain B Binding Site BS01

Receptor Information
>4fir Chain B (length=333) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDKLKIIMEKGTERLKRGFAKMVKGGVIMDVTNAEQARIAEEAGAVAVMA
LHKVPADIRKAGGVARMAPVEKIQEIMDAVTIPVMAKCRIGHEAEARILE
ALGVDMIDESEVLTPADPFFHIYKKKFTAPFVCGARNLGEAVRRIWEGAA
MIRTKGEAGTGNIIEAVRHVRLVNENIRLIQRMTDEEIYGVAEKFAEPYL
RLAFSVKEISGLPKRVLENEPIYEGFTYREIVEDIYKILLEIKKLGRLPV
VNFAAGGVATPADAALMMAMGMDGVFVGSGIFKSSNPPKMARAIVEAVNH
WDEPDVLAEISREIGEPMRGQAIEELQVRMEER
Ligand information
Ligand IDR5P
InChIInChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)/t3-,4+,5-/m0/s1
InChIKeyPPQRONHOSHZGFQ-LMVFSUKVSA-N
SMILES
SoftwareSMILES
CACTVS 3.370O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H](O)C=O
CACTVS 3.370O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)C=O
ACDLabs 12.01O=P(OCC(O)C(O)C(O)C=O)(O)O
OpenEye OEToolkits 1.7.6C(C(C(C(C=O)O)O)O)OP(=O)(O)O
FormulaC5 H11 O8 P
NameRIBOSE-5-PHOSPHATE
ChEMBL
DrugBankDB02053
ZINCZINC000022116391
PDB chain4fir Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4fir Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		D30 P55 K87 V112 R153 A158 G159 G257 G278 S279
Binding residue
(residue number reindexed from 1)		D30 P55 K87 V112 R153 A158 G159 G257 G278 S279
Annotation score5
Enzymatic activity
Enzyme Commision number 4.3.3.6: pyridoxal 5'-phosphate synthase (glutamine hydrolyzing).
Gene Ontology
Molecular Function
GO:0016829 lyase activity
GO:0016843 amine-lyase activity
GO:0036381 pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
Biological Process
GO:0006520 amino acid metabolic process
GO:0008615 pyridoxine biosynthetic process
GO:0042819 vitamin B6 biosynthetic process
GO:0042823 pyridoxal phosphate biosynthetic process

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:4fir, PDBe:4fir, PDBj:4fir
PDBsum4fir
PubMed23104439
UniProtO59080|PDXS_PYRHO Pyridoxal 5'-phosphate synthase subunit PdxS (Gene Name=pdxS)

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