Structure of PDB 4iy7 Chain D Binding Site BS04

Receptor Information

>4iy7 Chain D (length=383) Species: 291331 (Xanthomonas oryzae pv. oryzae KACC 10331)

ALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHN
PTRFAYERCVAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYG
GTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPML
KLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLN
GHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPL
RMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIV
SIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARR
EQLGISDALVRLSVGIEDLGDLRGDLERALVNQ

Ligand information

• Ligand ID: PYR
• InChI: InChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6)
• InChIKey: LCTONWCANYUPML-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: CC(=O)C(O)=O
  OpenEye OEToolkits 1.7.6: CC(=O)C(=O)O
  ACDLabs 12.01: O=C(C(=O)O)C
• Formula: C3 H4 O3
• Name: PYRUVIC ACID
• ChEMBL: CHEMBL1162144
• DrugBank: DB00119
• ZINC: ZINC000001532517
• PDB chain: 4iy7 Chain D Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4iy7 PLP undergoes conformational changes during the course of an enzymatic reaction.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): N271 E380 D381 L382
• Binding residue (residue number reindexed from 1): N258 E367 D368 L369
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): R60 Y112 D185 K210
• Catalytic site (residue number reindexed from 1): R47 Y99 D172 K197
• Enzyme Commision number: 4.4.1.1: cystathionine gamma-lyase.

Gene Ontology

Molecular Function

• GO:0003962 cystathionine gamma-synthase activity
• GO:0016846 carbon-sulfur lyase activity
• GO:0030170 pyridoxal phosphate binding

Biological Process

• GO:0019346 transsulfuration

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:4iy7, PDBe:4iy7, PDBj:4iy7
• PDBsum: 4iy7
• PubMed: 24531493
• UniProt: Q5H4T8