Structure of PDB 2ys6 Chain A Binding Site BS01

Receptor Information

>2ys6 Chain A (length=421) Species: 1462 (Geobacillus kaustophilus)

NLYFQSHMNVLVIGRGGREHAIAWKAAQSPLVGKLYVAPGNPGIADVAEL
VHIDELDIEALVQFAKQQAIDLTIVGPEAPLASGIVDRFMAEGLRIFGPS
QRAALIEGSKAFAKELMKKYGIPTADHAAFTSYEEAKAYIEQKGAPIVIK
ADGKGVTVAQTVEEALAAAKAALVDGQFGTAGSQVVIEEYLEGEEFSFMA
FVNGEKVYPLAIAQDHKRAYDGDEGPNTGGMGAYSPVPQISDEMMDAALE
AILRPAAKALAAEGRPFLGVLYAGLMATANGPKVIEFNARFGDPEAQVVL
PRLKTDLVEAVLAVMDGKELELEWTDEAVLGVVLAAKGYPGAYERGAEIR
GLDRISPDALLFHAGTKREGGAWYTNGGRVLLLAAKGETLAKAKEKAYEQ
LAAIDCDGLFYRRDIGRRAIE

Ligand information

• Ligand ID: GLY
• InChI: InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)
• InChIKey: DHMQDGOQFOQNFH-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C(C(=O)O)N
  CACTVS 3.341: NCC(O)=O
  ACDLabs 10.04: O=C(O)CN
• Formula: C2 H5 N O2
• Name: GLYCINE
• ChEMBL: CHEMBL773
• DrugBank: DB00145
• ZINC: ZINC000004658552
• PDB chain: 2ys6 Chain A Residue 431

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2ys6 Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria
• Resolution: 2.21 Å
• Binding residue (original residue number in PDB): D212 G226 Y269 R287 D290 E292
• Binding residue (residue number reindexed from 1): D215 G229 Y272 R290 D293 E295
• Annotation score: 5

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:2ys6, PDBe:2ys6, PDBj:2ys6
• PDBsum: 2ys6
• PubMed: 20716513
• UniProt: Q5L3C7