Structure of PDB 3der Chain D Binding Site BS03

Receptor Information
>3der Chain D (length=341) Species: 243274 (Thermotoga maritima MSB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RIVNVKLSLKRYEYEKPFHITGSVSSESRNVEVEIVLESGVKGYGEASPS
FRVNGERVEALLAIENAVREMITGIDVRNYARIFEITDRLFGFPSLKAAV
QFATLDALSQELGTQVCYLLGGKRDEIETDKTVGIDTVENRVKEAKKIFE
EGFRVIKIKVGENLKEDIEAVEEIAKVTRGAKYIVDANMGYTQKEAVEFA
RAVYQKGIDIAVYEQPVRREDIEGLKFVRFHSPFPVAADESARTKFDVMR
LVKEEAVDYVNIKLMKSGISDALAIVEIAESSGLKLMIGCMGESSLGINQ
SVHFALGTGAFEFHDLDSHLMLKEEVFRGKFIQDGPRMRVK
Ligand information
Ligand IDLYS
InChIInChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+1/t5-/m0/s1
InChIKeyKDXKERNSBIXSRK-YFKPBYRVSA-O
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCCC[NH3+])C(O)=O
ACDLabs 10.04O=C(O)C(N)CCCC[NH3+]
OpenEye OEToolkits 1.5.0C(CC[NH3+])C[C@@H](C(=O)O)N
CACTVS 3.341N[C@@H](CCCC[NH3+])C(O)=O
OpenEye OEToolkits 1.5.0C(CC[NH3+])CC(C(=O)O)N
FormulaC6 H15 N2 O2
NameLYSINE
ChEMBL
DrugBank
ZINC
PDB chain3der Chain D Residue 412 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3der Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		K161 D188 D241 K265 C292
Binding residue
(residue number reindexed from 1)		K159 D186 D239 K263 C290
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) F20 T134 K159 K161 D188 E216 D241 E242 S243 K265 G291 C292 M293 H316 D317 L318
Catalytic site (residue number reindexed from 1) F18 T132 K157 K159 D186 E214 D239 E240 S241 K263 G289 C290 M291 H314 D315 L316
Enzyme Commision number 5.1.1.20: L-Ala-D/L-Glu epimerase.
Gene Ontology
Molecular Function
GO:0016853 isomerase activity
GO:0016854 racemase and epimerase activity
GO:0016855 racemase and epimerase activity, acting on amino acids and derivatives
GO:0046872 metal ion binding
GO:0103031 L-Ala-D/L-Glu epimerase activity
Biological Process
GO:0016998 cell wall macromolecule catabolic process
GO:0071555 cell wall organization

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3der, PDBe:3der, PDBj:3der
PDBsum3der
PubMed19000819
UniProtQ9WXM1|AEEP_THEMA L-Ala-D/L-Glu epimerase (Gene Name=TM_0006)

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