Structure of PDB 4rkd Chain E Binding Site BS03

Receptor Information

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

MFERIDYYAGDPILGLVEKFAADNNPDKVNLGIGIYYDESGVMPVLDCVK
IAEQRIADPISPRPYLPMAGLPGHRKGCQELLFGKDAPVLKDGLVATIAT
IGGSGALKVGAEFIHEWFPQSKCYVSDPTWGNHIAIFEGCDIEVGKYPYY
DTATGGIKFDEMIAFFETLNKDDVLLLHPCCHNPTGVDLTREQWDTVLNV
IQERELIPFMDIAYQGFGEDMDSDAYAIRKAVDMGLPLFVSNSFSKNLSL
YGERVGGLSVVCPTVDETERVFGQLNSTVRRIYSSPPSHGGRVVDIVMND
AALHEQWVGEVYAMRDRIKSMRTKLKSVLEAKISGRNFDYLTAQNGMFSF
TGLTPEQVERLQSEFGIYMISNSRMCVAGLNSSNIDYVANAMVDVLKD

Ligand information

• Ligand ID: KET
• InChI: InChI=1S/C12H15N2O9P/c1-6-11(17)8(4-14-9(12(18)19)2-10(15)16)7(3-13-6)5-23-24(20,21)22/h3-4,9,17H,2,5H2,1H3,(H,15,16)(H,18,19)(H2,20,21,22)/p+1/b14-4+/t9-/m0/s1
• InChIKey: OEULMZWKJBFRJF-LPQZUGQSSA-O
• SMILES:
  CACTVS 3.341: Cc1[nH+]cc(CO[P](O)(O)=O)c(C=N[C@@H](CC(O)=O)C(O)=O)c1O
  OpenEye OEToolkits 1.5.0: Cc1c(c(c(c[nH+]1)COP(=O)(O)O)C=NC(CC(=O)O)C(=O)O)O
  CACTVS 3.341: Cc1[nH+]cc(CO[P](O)(O)=O)c(C=N[CH](CC(O)=O)C(O)=O)c1O
  ACDLabs 10.04: O=C(O)CC(/N=C/c1c(c[nH+]c(c1O)C)COP(=O)(O)O)C(=O)O
• Formula: C12 H16 N2 O9 P
• Name: 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYLENE)-AMINO]-SUCCINIC ACID;
  PYRIDOXYLIDENE-ASPARTIC ACID-5-MONOPHOSPHATE
• PDB chain: 4rkd Chain E Residue 404

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): G34 G102 G103 S104 W130 N183 Y214 S243 S245 K246 R254
• Binding residue (residue number reindexed from 1): G34 G102 G103 S104 W130 N183 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