Structure of PDB 4rkd Chain A Binding Site BS01

Receptor Information

>4rkd Chain A (length=398) Species: 408968 (Psychrobacter sp. B6)

MFERIDYYAGDPILGLVEKFAADNNPDKVNLGIGIYYDESGVMPVLDCVK
IAEQRIADPISPRPYLPMAGLPGHRKGCQELLFGKDAPVLKDGLVATIAT
IGGSGALKVGAEFIHEWFPQSKCYVSDPTWGNHIAIFEGCDIEVGKYPYY
DTATGGIKFDEMIAFFETLNKDDVLLLHPCCHNPTGVDLTREQWDTVLNV
IQERELIPFMDIAYQGFGEDMDSDAYAIRKAVDMGLPLFVSNSFSKNLSL
YGERVGGLSVVCPTVDETERVFGQLNSTVRRIYSSPPSHGGRVVDIVMND
AALHEQWVGEVYAMRDRIKSMRTKLKSVLEAKISGRNFDYLTAQNGMFSF
TGLTPEQVERLQSEFGIYMISNSRMCVAGLNSSNIDYVANAMVDVLKD

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: 4rkd Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4rkd Crystal structure and enzymatic properties of a broad substrate-specificity psychrophilic aminotransferase from the Antarctic soil bacterium Psychrobacter sp. B6.
• Resolution: 2.76 Å
• Binding residue (original residue number in PDB): G102 G103 S104 W130 D211 A213 Y214 S243 S245 K246 R254
• Binding residue (residue number reindexed from 1): G102 G103 S104 W130 D211 A213 Y214 S243 S245 K246 R254
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): W130 D211 A213 K246
• Catalytic site (residue number reindexed from 1): W130 D211 A213 K246
• Enzyme Commision number: 2.6.1.-

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004838 L-tyrosine-2-oxoglutarate transaminase activity
• GO:0008483 transaminase activity
• GO:0030170 pyridoxal phosphate binding
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006520 amino acid metabolic process
• GO:0009058 biosynthetic process
• GO:0033585 L-phenylalanine biosynthetic process from chorismate via phenylpyruvate

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:4rkd, PDBe:4rkd, PDBj:4rkd
• PDBsum: 4rkd
• PubMed: 25760611
• UniProt: C7E5X4