Structure of PDB 2yrx Chain A Binding Site BS01

Receptor Information

>2yrx Chain A (length=420) Species: 1462 (Geobacillus kaustophilus)

NLYFQSHMNVLVIGRGGREHAIAWKAAQSPLVGKLYVAPGNPGIADVAEL
VHIDELDIEALVQFAKQQAIDLTIVGPEAPLASGIVDRFMAEGLRIFGPS
QRAALIEGSKAFAKELMKKYGIPTADHAAFTSYEEAKAYIEQKGAPIVIK
ADGKGVTVAQTVEEALAAAKAALVDGQFGTAGSQVVIEEYLEGEEFSFMA
FVNGEKVYPLAIAQDHKRAYDGDEGPNTGGMGAYSPVPQISDEMMDAALE
AILRPAAKALAAEGRPFLGVLYAGLMATANGPKVIEFNARFGDPEAQVVL
PRLKTDLVEAVLAVMDGKELELEWTDEAVLGVVLAAKGYPGAYERGAEIR
GLDRISPDALLFHAGTKREGGAWYTNGGRVLLLAAKGETLAKAKEKAYEQ
LAAIDCDGLFYRRDIGRRAI

Ligand information

• Ligand ID: PO4
• InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
• InChIKey: NBIIXXVUZAFLBC-UHFFFAOYSA-K
• SMILES:
  CACTVS 3.341: [O-][P]([O-])([O-])=O
  ACDLabs 10.04: [O-]P([O-])([O-])=O
  OpenEye OEToolkits 1.5.0: [O-]P(=O)([O-])[O-]
• Formula: O4 P
• Name: PHOSPHATE ION
• DrugBank: DB14523
• PDB chain: 2yrx Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2yrx Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): R11 R287 R376
• Binding residue (residue number reindexed from 1): R18 R290 R379
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 6.3.4.13: phosphoribosylamine--glycine ligase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004637 phosphoribosylamine-glycine ligase activity
• GO:0005524 ATP binding
• GO:0016874 ligase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006164 purine nucleotide biosynthetic process
• GO:0006189 'de novo' IMP biosynthetic process
• GO:0009113 purine nucleobase biosynthetic process

External links

• PDB: RCSB:2yrx, PDBe:2yrx, PDBj:2yrx
• PDBsum: 2yrx
• PubMed: 20716513
• UniProt: Q5L3C7