Structure of PDB 4a0r Chain A Binding Site BS01

Receptor Information
>4a0r Chain A (length=755) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PFHLPLNHPTYLIWSANTSLGKTLVSTGIAASFLLQQPSSSATKLLYLKP
IQTGFPSDSDSRFVFSKLDSLSLRRQIPISISNSVLHSSLPAAKSLGLNV
EVSESGMCSLNFRDEKTVTGAPELLCKTLYAWEAAISPHLAAERENATVE
DSVVLQMIEKCLKEEMDLLCLVETAGGVASPGPSGTLQCDLYRPFRLPGI
LVGDGRLGGISGTIAAYESLKLRGYDIAAVVFEDHGLVNEVPLTSYLRNK
VPVLVLPPVPKDPSDDLIEWFVESDGVFKALKETMVLANLERLERLNGMA
KLAGEVFWWPFTQHKLVHQETVTVIDSRCGENFSIYKASDNSSLSQQFDA
CASWWTQGPDPTFQAELAREMGYTAARFGHVMFPENVYEPALKCAELLLD
GVGKGWASRVYFSDNGSTAIEIALKMAFRKFCVDHNFIVVKVIALRGSYH
GDTLGAMEAQAPSPYTGFLQQPWYTGRGLFLDPPTVFLSNGSWNISLTFT
SRDEIFDKSRDASTLARIYSAYLSKHLAHVGALIIEPVIHGAGGMHMVDP
LFQRVLVNECRNRKIPVIFDEVFTGFWRLGVETTTELLGCKPDIACFAKL
LTGGMVPLAVTLATDAVFDSFSGDSKLKALLHGHSYSAHAMGCATAAKAI
QWFKDPETNHNITSQGKTLRELWDEELVQQISSHSAVQRVVVIGTLFALE
LKSLYAKSLLIMLREDGIFTRPLGNVIYLMCGPCTSPEICRRLLTKLYKR
LGEFN
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 chain4a0r Chain A Residue 1644 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4a0r Biochemical and Structural Characterization of the Arabidopsis Bifunctional Enzyme Dethiobiotin Synthetase-Diaminopelargonic Acid Aminotransferase: Evidence for Substrate Channeling in Biotin Synthesis.
Resolution2.68 Å
Binding residue
(original residue number in PDB)		N430 G431 S432 Y473 H474 E581 D615 V617 K644
Binding residue
(residue number reindexed from 1)		N415 G416 S417 Y449 H450 E536 D570 V572 K599
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) F326 Y473 D615 K644
Catalytic site (residue number reindexed from 1) F311 Y449 D570 K599
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:4a0r, PDBe:4a0r, PDBj:4a0r
PDBsum4a0r
PubMed22547782
UniProtB0F481|BIODA_ARATH Bifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial (Gene Name=BIO3-BIO1)

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