Structure of PDB 2zdh Chain A

Receptor sequence
>2zdhA (length=319) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence]
MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKAL
TALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGK
PYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPF
FVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEV
GVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETV
QELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFE
AGGVAYPELLRRLVELALT
3D structure
PDB2zdh Crystal structure of D-Alanine:D-Alanine Ligase with ADP and D-Alanine from Thermus thermophius HB8
ChainA
Resolution1.9 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) E13 V16 L19 H82 S159 E226 Y229 R268 D270 E282 N284 G288 T292
Catalytic site (residue number reindexed from 1) E13 V16 L19 H82 S159 E226 Y229 R268 D270 E282 N284 G288 T292
Enzyme Commision number 6.3.2.4: D-alanine--D-alanine ligase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 MG A E282 N284 E282 N284
BS02 ADP A K116 F151 K153 G158 S159 S160 I163 E189 L192 E197 Y223 K228 F272 E282 K116 F151 K153 G158 S159 S160 I163 E189 L192 E197 Y223 K228 F272 E282
BS03 DAL A E13 Y229 R268 G288 E13 Y229 R268 G288
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:2zdh, PDBe:2zdh, PDBj:2zdh
PDBsum2zdh
PubMed
UniProtQ5SHZ3|DDL_THET8 D-alanine--D-alanine ligase (Gene Name=ddl)

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