Structure of PDB 4a0f Chain B Binding Site BS02

Receptor Information
>4a0f Chain B (length=750) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VSPFHLPLNHPTYLIWSANTSLGKTLVSTGIAASFLLQQSATKLLYLKPI
QTGFPSDSDSRFVFSKLDSLSLRRQIPISISNSVLHSSLPAAKSLGLESG
MCSLNFRDEKTVTGAPELLCKTLYAWEAAISPHLAAERENATVEDSVVLQ
MIEKCLKEEMDLLCLVETAGGVASPGPSGTLQCDLYRPFRLPGILVGDGR
LGGISGTIAAYESLKLRGYDIAAVVFEDHGLVNEVPLTSYLRNKVPVLVL
PPVPKDPSDDLIEWFVESDGVFKALKETMVLANLERLERLNGMAKLAGEV
FWWPYTQHKLVHQETVTVIDSRCGENFSIYKASDNSSLSQQFDACASWWT
QGPDPTFQAELAREMGYTAARFGHVMFPENVYEPALKCAELLLDGVGKGW
ASRVYFSDNGSTAIEIALKMAFRKFCVDHNFIVVKVIALRGSYHGDTLGA
MEAQAPSPYTGFLQQPWYTGRGLFLDPPTVFLSNGSWNISLPESFTFTSR
DEIFDKSRDASTLARIYSAYLSKHAHVGALIIEPVIHGAGGMHMVDPLFQ
RVLVNECRNRKIPVIFDEVFTGFWRLGVETTTELLGCKPDIACFAKLLTG
GMVPLAVTLATDAVFDSFSGDSKLKALLHGHSYSAHAMGCATAAKAIQWF
KDPETNHNITSQGKTLRELWDEELVQQISSHSAVQRVVVIGTLFALELSL
YAKSLLIMLREDGIFTRPLGNVIYLMCGPCTSPEICRRLLTKLYKRLGEF
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 chain4a0f Chain B Residue 1644 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4a0f Biochemical and Structural Characterization of the Arabidopsis Bifunctional Enzyme Dethiobiotin Synthetase-Diaminopelargonic Acid Aminotransferase: Evidence for Substrate Channeling in Biotin Synthesis.
Resolution2.714 Å
Binding residue
(original residue number in PDB)		G431 S432 Y473 H474 E581 D615 V617 K644
Binding residue
(residue number reindexed from 1)		G410 S411 Y443 H444 E533 D567 V569 K596
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y326 Y473 D615 K644
Catalytic site (residue number reindexed from 1) Y305 Y443 D567 K596
Enzyme Commision number 2.6.1.62: adenosylmethionine--8-amino-7-oxononanoate transaminase.
6.3.3.3: dethiobiotin synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004015 adenosylmethionine-8-amino-7-oxononanoate transaminase activity
GO:0004141 dethiobiotin synthase activity
GO:0005524 ATP binding
GO:0008483 transaminase activity
GO:0016874 ligase activity
GO:0030170 pyridoxal phosphate binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
Biological Process
GO:0009102 biotin biosynthetic process
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4a0f, PDBe:4a0f, PDBj:4a0f
PDBsum4a0f
PubMed22547782
UniProtB0F481|BIODA_ARATH Bifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial (Gene Name=BIO3-BIO1)

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