Structure of PDB 5k30 Chain A Binding Site BS01

Receptor Information
>5k30 Chain A (length=386) Species: 546 (Citrobacter freundii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SDCRTYGFNTQIVHAGQQPDPSTGALSTPIFQTSTFVFDSAEQGAARFRL
GNPTTDALEKKLAVLERGEAGLATASGISAITTTLLTLCQQGDHIVSASA
IYGCTHAFLSHSMPKFGINVSFVDAAKPEEIRAAMRPETKVVYIETPANP
TLSLVDIETVAGIAHQQGALLVVDNTFMSPYCQQPLQLGADIVVHSVTKY
INGHGDVIGGIIVGKQEFIDQARFVGLKDITGGCMSPFNAWLTLRGVKTL
GIRMERHCENALKIARFLEGHPSITRVYYPGLSSHPQYELGQRQMSLPGG
IISFEIAGGLEAGRRMINSVELCLLAVSLGDTETLIQHPASMTHSPVAPE
ERLKAGITDGLIRLSVGLEDPEDIINDLEHAIRKAT
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 chain5k30 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5k30 Sulfoxides of sulfur-containing amino acids are suicide substrates of Citrobacter freundii methionine gamma-lyase. Structural bases of the enzyme inactivation.
Resolution1.59 Å
Binding residue
(original residue number in PDB)		G88 I89 Y113 E156 D185 T187 F188 S207 T209 K210
Binding residue
(residue number reindexed from 1)		G77 I78 Y102 E145 D174 T176 F177 S196 T198 K199
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R60 Y113 D185 K210
Catalytic site (residue number reindexed from 1) R49 Y102 D174 K199
Enzyme Commision number 4.4.1.11: methionine gamma-lyase.
Gene Ontology
Molecular Function
GO:0016829 lyase activity
GO:0016846 carbon-sulfur lyase activity
GO:0018826 methionine gamma-lyase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0019346 transsulfuration
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5k30, PDBe:5k30, PDBj:5k30
PDBsum5k30
PubMed31711941
UniProtA0A0A5P8W7

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