Structure of PDB 5m3z Chain A Binding Site BS03

Receptor Information
>5m3z Chain A (length=395) Species: 546 (Citrobacter freundii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DCRTYGFNTQIVHAGQQPDPSTGALSTPIFQTSTFVFDSAEQGAARFALE
ESGYIYTRLGNPTTDALEKKLAVLERGEAGLATASGISAITTTLLTLCQQ
GDHIVSASAIYGHTHAFLSHSMPKFGINVSFVDAAKPEEIRAAMRPETKV
VYIETPANPTLSLVDIETVAGIAHQQGALLVVDNTFMSPYCQQPLQLGAD
IVVHSVTKYINGHGDVIGGIIVGKQEFIDQARFVGLKDITGGCMSPFNAW
LTLRGVKTLGIRMERHCENALKIARFLEGHPSITRVYYPGLSSHPQYELG
QRQMSLPGGIISFEIAGGLEAGRRMINSVELCLLAVSLGDTETLIQHPAS
MTHSPVAPEERLKAGITDGLIRLSVGLEDPEDIINDLEHAIRKAT
Ligand information
Ligand IDPY6
InChIInChI=1S/C14H23N2O7P/c1-3-4-5-12(14(18)19)16-7-11-10(8-23-24(20,21)22)6-15-9(2)13(11)17/h6,12,16-17H,3-5,7-8H2,1-2H3,(H,18,19)(H2,20,21,22)/t12-/m0/s1
InChIKeyNHVFCSUYJRWFNW-LBPRGKRZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCC[C@H](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O
ACDLabs 10.04O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)CCCC
OpenEye OEToolkits 1.5.0CCCC[C@@H](C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O)O
OpenEye OEToolkits 1.5.0CCCCC(C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O)O
CACTVS 3.341CCCC[CH](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O
FormulaC14 H23 N2 O7 P
Name2-[O-PHOSPHONOPYRIDOXYL]-AMINO-HEXANOIC ACID;
VITAMIN B6 COMPLEXED WITH 2-AMINO-HEXANOIC ACID
ChEMBL
DrugBankDB02981
ZINCZINC000002047161
PDB chain5m3z Chain A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5m3z Crystal structure of mutant form Cys115His of Citrobacter freundii methionine gamma-lyase complexed with l-norleucine.
Resolution1.45 Å
Binding residue
(original residue number in PDB)		G88 I89 Y113 D185 S207 T209 K210 V338 S339 R374
Binding residue
(residue number reindexed from 1)		G86 I87 Y111 D183 S205 T207 K208 V336 S337 R372
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R60 Y113 D185 K210
Catalytic site (residue number reindexed from 1) R58 Y111 D183 K208
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5m3z, PDBe:5m3z, PDBj:5m3z
PDBsum5m3z
PubMed28602917
UniProtA0A0A5P8W7

[Back to BioLiP]