Structure of PDB 4rkd Chain C Binding Site BS01

Receptor Information
>4rkd Chain C (length=398) Species: 408968 (Psychrobacter sp. B6) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MFERIDYYAGDPILGLVEKFAADNNPDKVNLGIGIYYDESGVMPVLDCVK
IAEQRIADPISPRPYLPMAGLPGHRKGCQELLFGKDAPVLKDGLVATIAT
IGGSGALKVGAEFIHEWFPQSKCYVSDPTWGNHIAIFEGCDIEVGKYPYY
DTATGGIKFDEMIAFFETLNKDDVLLLHPCCHNPTGVDLTREQWDTVLNV
IQERELIPFMDIAYQGFGEDMDSDAYAIRKAVDMGLPLFVSNSFSKNLSL
YGERVGGLSVVCPTVDETERVFGQLNSTVRRIYSSPPSHGGRVVDIVMND
AALHEQWVGEVYAMRDRIKSMRTKLKSVLEAKISGRNFDYLTAQNGMFSF
TGLTPEQVERLQSEFGIYMISNSRMCVAGLNSSNIDYVANAMVDVLKD
Ligand information
Ligand IDPLP
InChIInChI=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)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain4rkd Chain C Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4rkd Crystal structure and enzymatic properties of a broad substrate-specificity psychrophilic aminotransferase from the Antarctic soil bacterium Psychrobacter sp. B6.
Resolution2.76 Å
Binding residue
(original residue number in PDB)		G102 G103 S104 W130 N183 D211 Y214 S243 S245 K246 R254
Binding residue
(residue number reindexed from 1)		G102 G103 S104 W130 N183 D211 Y214 S243 S245 K246 R254
Annotation score1
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4rkd, PDBe:4rkd, PDBj:4rkd
PDBsum4rkd
PubMed25760611
UniProtC7E5X4

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