Structure of PDB 5x2z Chain D Binding Site BS01

Receptor Information
>5x2z Chain D (length=396) Species: 303 (Pseudomonas putida) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSNKLPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPTVEYGAACFAG
EQAGHFYSRISNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLR
PGDEVLLGNTLYGHTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATR
VIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGA
DLVVHSATKYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDA
ALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPGLASFPQYTL
ARQQMSQPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPA
SMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA
Ligand information
Ligand ID3LM
InChIInChI=1S/C13H19N2O7PS/c1-8-12(16)10(6-15-11(13(17)18)3-4-24-2)9(5-14-8)7-22-23(19,20)21/h3,5,15-16H,4,6-7H2,1-2H3,(H,17,18)(H2,19,20,21)/b11-3+
InChIKeyLPFNPHQQDYAHKU-QDEBKDIKSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CSCC=C(NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O
OpenEye OEToolkits 1.7.0Cc1c(c(c(cn1)COP(=O)(O)O)CNC(=CCSC)C(=O)O)O
OpenEye OEToolkits 1.7.0Cc1c(c(c(cn1)COP(=O)(O)O)CN/C(=C/CSC)/C(=O)O)O
CACTVS 3.370CSC\C=C(NCc1c(O)c(C)ncc1CO[P](O)(O)=O)/C(O)=O
ACDLabs 12.01O=P(O)(O)OCc1cnc(c(O)c1CNC(=C/CSC)/C(=O)O)C
FormulaC13 H19 N2 O7 P S
Name(2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-4-(methylsulfanyl)but-2-enoic acid
ChEMBL
DrugBank
ZINCZINC000103526166
PDB chain5x2z Chain D Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5x2z Structural and mechanistic insights into homocysteine degradation by a mutant of methionine gamma-lyase based on substrate-assisted catalysis
Resolution1.8 Å
Binding residue
(original residue number in PDB)		G89 M90 Y114 N161 D186 S208 K211 V339 S340 L341 T355 R375
Binding residue
(residue number reindexed from 1)		G87 M88 Y112 N159 D184 S206 K209 V337 S338 L339 T353 R373
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R61 Y114 D186 K211
Catalytic site (residue number reindexed from 1) R59 Y112 D184 K209
Enzyme Commision number 4.4.1.11: methionine gamma-lyase.
4.4.1.2: homocysteine desulfhydrase.
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
GO:0047982 homocysteine desulfhydrase activity
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:5x2z, PDBe:5x2z, PDBj:5x2z
PDBsum5x2z
PubMed28329912
UniProtP13254|MEGL_PSEPU L-methionine gamma-lyase (Gene Name=mdeA)

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