3r5f Summary

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Crystal structure of D-alanine-D-alnine ligase from Xanthomonas oryzae pv. oryzae with ATP

A publication describing this structure is not available. The depositing authors are Doan, T.T.N.search; Kim, J.K.search; Kang, L.W.search

This crystal structure was determined using X-ray diffraction at a resolution of 2.07 Å and deposited in 2011.

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

The PDB entry contains the structure of D-alanine--D-alanine ligase 1. This molecule has the UniProt identifier Q2P8P8 (Q2P8P8_XANOM)search. The sample contained 384 residues which is 100% of the natural sequence. Out of 384 residues 343 were observed and are deposited in the PDB.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

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 1 Q2P8P8 (1-367) (Q2P8P8_XANOM)search Xanthomonas oryzae pv. oryzae MAFF 311018search 100% 384 89%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
Q2P8P8 (1 - 367) D-alanine--D-alanine ligase 1 Xanthomonas oryzae pv. oryzae KACC 10331

Chain Sequence family (Pfam)
A (Q2P8P8) PF01820: D-ala D-ala ligase N-terminussearch, PF07478: D-ala D-ala ligase C-terminussearch

Chain ID Molecular function (GO) Biological process (GO) Cellular component (GO)
A (Q2P8P8) ATP bindingsearch D-alanine-D-alanine ligase activitysearch metal ion bindingsearch catalytic activitysearch magnesium ion bindingsearch manganese ion bindingsearch nucleotide bindingsearch ligase activitysearch peptidoglycan biosynthetic processsearch regulation of cell shapesearch cytoplasmsearch

Chain InterPro annotation
A 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