3k3p Summary

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Crystal Structure of the Apo Form of D-Alanine:D-Alanine Ligase (DDl) from Streptococcus mutans

The structure was published by Lu, Y., Xu, H., and Zhao, X., in 2010 in a paper entitled "Crystal structure of the Apo form of D-Alanine:D-Alanine ligase (DDl) from Streptococcus mutans" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.23 Å and deposited in 2009.

The experimental data on which the structure is based was also deposited.

This PDB entry contains multiple copies of the structure of D-alanine--D-alanine ligase.

The molecule most likely forms homodimers.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A D-alanine--D-alanine ligase P95803 (1-349) (DDL_STRMU)search Streptococcus mutans UA159search 100% 383 83%
B D-alanine--D-alanine ligase P95803 (1-349) (DDL_STRMU)search Streptococcus mutans UA159search 100% 383 83%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
P95803 (1 - 349) D-alanine--D-alanine ligase Streptococcus mutans

Chain Sequence family (Pfam)
A, B (P95803) PF01820: D-ala D-ala ligase N-terminussearch, PF07478: D-ala D-ala ligase C-terminussearch

Chain ID Molecular function (GO) Cellular component (GO) Biological process (GO)
A, B (P95803) catalytic activitysearch ATP bindingsearch nucleotide bindingsearch manganese ion bindingsearch D-alanine-D-alanine ligase activitysearch metal ion bindingsearch ligase activitysearch magnesium ion bindingsearch cytoplasmsearch peptidoglycan biosynthetic processsearch cell wall organizationsearch regulation of cell shapesearch

Chain InterPro annotation
A, B D-alanine--D-alanine ligase/VANA/B/C, conserved sitesearch D-alanine--D-alanine ligasesearch D-alanine--D-alanine ligase, C-terminalsearch D-alanine--D-alanine ligase, N-terminal domainsearch ATP-grasp foldsearch ATP-grasp fold, subdomain 1search ATP-grasp fold, subdomain 2search Pre-ATP-grasp domainsearch