Structure of PDB 5bpf Chain B

Receptor sequence
>5bpfB (length=301) Species: 632 (Yersinia pestis) [Search protein sequence]
MAEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQL
KEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRT
KLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHSVG
MSKVDHASELQKALVEAFQDSDVLIEKWLSGPEFTVAILGDEVLPSIRIQ
PPGVFYDYDAKLSDKTQYFCPSGLSDESEQQLAALALQAYHALDCSGWGR
VDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILMLA
D
3D structure
PDB5bpf Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.
ChainB
Resolution2.28 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) E15 V18 L21 H63 D213 R255 D257 E270 N272 G276 H280
Catalytic site (residue number reindexed from 1) E15 V18 L21 H63 D209 R250 D252 E265 N267 G271 H275
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 ADP B K97 K144 S151 M154 E180 W182 L183 E187 Y210 M259 E270 K97 K144 S148 M151 E176 W178 L179 E183 Y206 M254 E265
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5bpf, PDBe:5bpf, PDBj:5bpf
PDBsum5bpf
PubMed26894530
UniProtQ8ZIE7|DDL_YERPE D-alanine--D-alanine ligase (Gene Name=ddl)

[Back to BioLiP]