2zdh Summary

pdbe.org/2zdh
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Crystal structure of D-Alanine:D-Alanine Ligase with ADP and D-Alanine from Thermus thermophius HB8

A publication describing this structure is not available. The depositing authors are Kitamuta, Y.search; Yokoyama, S.search; Kuramitsu, S.search; RIKEN Structural Genomics/Proteomics Initiative (RSGI)search

This crystal structure was determined using X-ray diffraction at a resolution of 1.9 Å and deposited in 2007.

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.

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 has more than one probable quaternary state observed. For more details see the quaternary structure page.

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 Q5SHZ3 (1-319) (DDL_THET8)search Thermus thermophilus HB8search 100% 319 100%
B D-alanine--D-alanine ligase Q5SHZ3 (1-319) (DDL_THET8)search Thermus thermophilus HB8search 100% 319 100%
C D-alanine--D-alanine ligase Q5SHZ3 (1-319) (DDL_THET8)search Thermus thermophilus HB8search 100% 319 100%
D D-alanine--D-alanine ligase Q5SHZ3 (1-319) (DDL_THET8)search Thermus thermophilus HB8search 100% 319 100%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
Q5SHZ3 (1 - 319) D-alanine--D-alanine ligase Thermus thermophilus HB8

Chain Sequence family (Pfam)
A, B, C, D (Q5SHZ3) 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, C, D (Q5SHZ3) ATP bindingsearch catalytic activitysearch D-alanine-D-alanine ligase activitysearch manganese ion bindingsearch magnesium ion bindingsearch ligase activitysearch metal ion bindingsearch nucleotide bindingsearch cytoplasmsearch peptidoglycan biosynthetic processsearch regulation of cell shapesearch cell wall organizationsearch

Chain InterPro annotation
A, B, C, D 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