Structure of PDB 2yky Chain C Binding Site BS01

Receptor Information

>2yky Chain C (length=431) Species: 398267 (Mesorhizobium sp. LUK)

SDTAEKAQAIAAARNTFARDNPVSAGHHERARRSMPGGNTRSILFHRPFP
LVIAQGTGSRFQDVDGHAYVNFLGEYTAGLFGHSHPVIRAAVERALAVGL
NLSTQTENEALFAEAVCDRFPSIDLVRFTNSGTEANLMALATATAITGRK
TVLAFDGGYHGGLLNFASGHAPTNAPYHVVLGVYNDVEGTADLLKRHGHD
CAAILVEPMLGAGGCVPAERAFLDLLRAEASRCGALLIFDEVMTSRLSGG
GAQEMLGISADLTTLGKYIGGGMSFGAFGGRRDLMERFDPARDGAFAHAG
TFNNNILTMSAGHAALTQIYTRQAASDLSASGDRFRANLNRIAVENQAPL
QFTGLGSLGTIHFSRAPIRSAGDVRAADQQLKELFFFHMLRKGIYLAPRG
MYALSLEIADAGRDAFAEALADFIGEQRALL

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: 2yky Chain C Residue 1447

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2yky Structural Determinants of the Beta-Selectivity of a Bacterial Aminotransferase.
• Resolution: 1.69 Å
• Binding residue (original residue number in PDB): G145 T146 Y172 H173 E220 D253 V255 M256 K280
• Binding residue (residue number reindexed from 1): G132 T133 Y159 H160 E207 D240 V242 M243 K267
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): N52 Y172 E220 D253 M256 K280 A416
• Catalytic site (residue number reindexed from 1): N39 Y159 E207 D240 M243 K267 A403

Gene Ontology

Molecular Function

• GO:0008483 transaminase activity
• GO:0030170 pyridoxal phosphate binding

External links

• PDB: RCSB:2yky, PDBe:2yky, PDBj:2yky
• PDBsum: 2yky
• PubMed: 22745123
• UniProt: A3EYF7