Structure of PDB 3vbe Chain D Binding Site BS01

Receptor Information

>3vbe Chain D (length=317) Species: 3847 (Glycine max)

STNIKKHVSQLIGRTPLVYLNKVTEGCGAYVAVKQEMMQPTASIKDRPAY
AMITDAEEKNLITPGKTTLIEPTSGNMGISMAFMAAMKGYKMVLTMPSYT
SLERRVTMRAFGAELILTDPAKGMGGTVKKAYELLENTPNAHMLQQFSNP
ANTQVHFETTGPEIWEDTNGQVDIFVMGIGSGGTVSGVGQYLKSKNPNVK
IYGVEPSESNVLNGGKPGPHHITGNGVGFKPDILDLDVMEKVLEVSSEDA
VNMARVLALKEGLMVGISSGANTVAALRLAQLPENKGKLIVTVHPSFGER
YLSSVLFQELRQEAENM

Ligand information

• Ligand ID: PLP
• InChI: InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
• InChIKey: NGVDGCNFYWLIFO-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
  OpenEye OEToolkits 1.5.0: Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
  ACDLabs 10.04: O=P(O)(O)OCc1cnc(c(O)c1C=O)C
• Formula: C8 H10 N O6 P
• Name: PYRIDOXAL-5'-PHOSPHATE;
  VITAMIN B6 Phosphate
• ChEMBL: CHEMBL82202
• DrugBank: DB00114
• ZINC: ZINC000001532514
• PDB chain: 3vbe Chain D Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3vbe Structure of Soybean beta-Cyanoalanine Synthase and the Molecular Basis for Cyanide Detoxification in Plants.
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): K95 M227 G230 S231 G232 G233 T234 S318 P345
• Binding residue (residue number reindexed from 1): K45 M177 G180 S181 G182 G183 T184 S268 P295
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K95 S124 E255 S259 S318 P345
• Catalytic site (residue number reindexed from 1): K45 S74 E205 S209 S268 P295
• Enzyme Commision number: 2.5.1.47: cysteine synthase.
  4.4.1.9: L-3-cyanoalanine synthase.

Gene Ontology

Molecular Function

• GO:0004124 cysteine synthase activity

Biological Process

• GO:0006535 cysteine biosynthetic process from serine

External links

• PDB: RCSB:3vbe, PDBe:3vbe, PDBj:3vbe
• PDBsum: 3vbe
• PubMed: 22739827
• UniProt: I1L6I6