Structure of PDB 1ibj Chain A Binding Site BS02

Receptor Information
>1ibj Chain A (length=380) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASVSTLLVNLDNKFDPFDAMSTPLYQTATFKQPSAIENGPYDYTRSGNPT
RDALESLLAKLDKADRAFCFTSGMAALSAVTHLIKNGEEIVAGDDVYGGS
DRLLSQVVPRSGVVVKRVNTTKLDEVAAAIGPQTKLVWLESPTNPRQQIS
DIRKISEMAHAQGALVLVDNSIMSPVLSRPLELGADIVMHSATKFIAGHS
DVMAGVLAVKGEKLAKEVYFLQNSEGSGLAPFDCWLCLRGIKTMALRIEK
QQENARKIAMYLSSHPRVKKVYYAGLPDHPGHHLHFSQAKGAGSVFSFIT
GSVALSKHLVETTKYFSIAVSFGSVKSLISMPCFMSHASIPAEVREARGL
TEDLVRISAGIEDVDDLISDLDIAFKTFPL
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 chain1ibj Chain A Residue 1400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ibj The three-dimensional structure of cystathionine beta-lyase from Arabidopsis and its substrate specificity
Resolution2.3 Å
Binding residue
(original residue number in PDB)		G157 M158 Y181 E224 D253 S275 T277 K278 M287 F406
Binding residue
(residue number reindexed from 1)		G73 M74 Y97 E140 D169 S191 T193 K194 M203 F322
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R129 Y181 D253 K278
Catalytic site (residue number reindexed from 1) R45 Y97 D169 K194
Enzyme Commision number 4.4.1.13: cysteine-S-conjugate beta-lyase.
Gene Ontology
Molecular Function
GO:0016829 lyase activity
GO:0030170 pyridoxal phosphate binding
GO:0042803 protein homodimerization activity
GO:0047804 cysteine-S-conjugate beta-lyase activity
GO:0060090 molecular adaptor activity
Biological Process
GO:0006555 methionine metabolic process
GO:0009086 methionine biosynthetic process
GO:0019279 L-methionine biosynthetic process from L-homoserine via cystathionine
GO:0019346 transsulfuration
GO:0071266 'de novo' L-methionine biosynthetic process
Cellular Component
GO:0009507 chloroplast
GO:0009570 chloroplast stroma

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1ibj, PDBe:1ibj, PDBj:1ibj
PDBsum1ibj
PubMed11402193
UniProtP53780|METC_ARATH Cystathionine beta-lyase, chloroplastic (Gene Name=At3g57050)

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