Structure of PDB 2gn2 Chain A Binding Site BS01

Receptor Information
>2gn2 Chain A (length=326) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ITYDLPVAIEDILEAKKRLAGKIYKTGMPRSNYFSERCKGEIFLKFENMQ
RTGSFKIRGAFNKLSSLTEAEKRKGVVACSAGNHAQGVSLSCAMLGIDGK
VVMPKGAPKSKVAATCDYSAEVVLHGDNFNDTIAKVSEIVETEGRIFIPP
YDDPKVIAGQGTIGLEIMEDLYDVDNVIVPIGGGGLIAGIAIAIKSINPT
IKVIGVQAENVHGMAASYYTGEITTHRTTGTLADGCDVSRPGNLTYEIVR
ELVDDIVLVSEDEIRNSMIALIQRNKVITEGAGALACAALLSGKLDSHIQ
NRKTVSIISGGNIDLSRVSQITGLVD
Ligand information
Ligand IDC5P
InChIInChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyIERHLVCPSMICTF-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
FormulaC9 H14 N3 O8 P
NameCYTIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL307679
DrugBankDB03403
ZINCZINC000003861744
PDB chain2gn2 Chain A Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2gn2 Crystal structures of Salmonella typhimurium biodegradative threonine deaminase and its complex with CMP provide structural insights into ligand-induced oligomerization and enzyme activation.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		R53 T54 G55 A116 D119 Y120 N314
Binding residue
(residue number reindexed from 1)		R51 T52 G53 A114 D117 Y118 N312
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K58 A83 Q209 V213 G215 G237 I310 S311
Catalytic site (residue number reindexed from 1) K56 A81 Q207 V211 G213 G235 I308 S309
Enzyme Commision number 4.3.1.17: L-serine ammonia-lyase.
4.3.1.19: threonine ammonia-lyase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003941 L-serine ammonia-lyase activity
GO:0004794 threonine deaminase activity
GO:0016829 lyase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0006520 amino acid metabolic process
GO:0006565 L-serine catabolic process
GO:0006567 threonine catabolic process
GO:0009097 isoleucine biosynthetic process
GO:0070689 L-threonine catabolic process to propionate

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2gn2, PDBe:2gn2, PDBj:2gn2
PDBsum2gn2
PubMed17046821
UniProtP11954|TDCB_SALTY L-threonine dehydratase catabolic TdcB (Gene Name=tdcB)

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