Structure of PDB 2yzm Chain C Binding Site BS01

Receptor Information
>2yzm Chain C (length=308) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKAL
TALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGK
PYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPF
FVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEV
GVLGNVFGEASPVGEVRYEAPRAELLIPAPLDPGTQETVQELALKAYKVL
GVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLR
RLVELALT
Ligand information
Ligand IDDAL
InChIInChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1
InChIKeyQNAYBMKLOCPYGJ-UWTATZPHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C(=O)O)N
CACTVS 3.341C[CH](N)C(O)=O
CACTVS 3.341C[C@@H](N)C(O)=O
ACDLabs 10.04O=C(O)C(N)C
OpenEye OEToolkits 1.5.0C[C@H](C(=O)O)N
FormulaC3 H7 N O2
NameD-ALANINE
ChEMBLCHEMBL66693
DrugBankDB01786
ZINCZINC000004658556
PDB chain2yzm Chain C Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2yzm Structure of D-Alanine:D-Alanine Ligase with substrate from Thermus thermophilus HB8
Resolution2.21 Å
Binding residue
(original residue number in PDB)		E13 E87 E282 N284
Binding residue
(residue number reindexed from 1)		E13 E87 E271 N273
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E13 V16 L19 H82 S159 R268 D270 E282 N284 G288 T292
Catalytic site (residue number reindexed from 1) E13 V16 L19 H82 S159 R257 D259 E271 N273 G277 T281
Enzyme Commision number 6.3.2.4: D-alanine--D-alanine ligase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0008716 D-alanine-D-alanine ligase activity
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2yzm, PDBe:2yzm, PDBj:2yzm
PDBsum2yzm
PubMed
UniProtQ5SHZ3|DDL_THET8 D-alanine--D-alanine ligase (Gene Name=ddl)

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