Structure of PDB 5nrh Chain B

Receptor sequence
>5nrhB (length=309) Species: 28450 (Burkholderia pseudomallei) [Search protein sequence]
IDPKRFGKVAVLLGGDSAEREVSLNSGRLVLQGLRDAGIDAHPFDPAQRP
LAALKDEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGLD
KFRTKLVWQQTGIPTPPFETVMRGDDYAARAQDIVAKLGVPLFVKPASEG
SSVAVEKVKSADALPAALEEAAKHDKIVIVEKSIEGGGEYTACIAADLDL
PLIRIVPAGEFYDYHAKYIANDTQYLIPCGLDAAKEAEFKRIARRAFDVL
GCTDWGRADFMLDAAGNPYFLEVNTAPGMTDHSLPPKAARAVGIGYSELV
VKVLSLTLD
3D structure
PDB5nrh Burkholderia pseudomallei d-alanine-d-alanine ligase; detailed characterisation and assessment of a potential antibiotic drug target.
ChainB
Resolution1.3 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) V25 N28 H70 H218 R260 G281 H285
Catalytic site (residue number reindexed from 1) V22 N25 H67 H215 R257 G278 H282
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 AMP B K104 F146 K148 S155 E184 S186 I187 E192 F214 Y215 L274 E275 K101 F143 K145 S152 E181 S183 I184 E189 F211 Y212 L271 E272
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:5nrh, PDBe:5nrh, PDBj:5nrh
PDBsum5nrh
PubMed31260169
UniProtQ63QJ9|DDL_BURPS D-alanine--D-alanine ligase (Gene Name=ddl)

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