Research workbench
Crystal structure of D-ALANINE:D-alanine ligase with ATP and D-ALANINE:D-alanine from thermus thermophius HB8
Analyse Crystal structure of D-ALANINE:D-alanine ligase with ATP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZDQ
- Type
- protein
- Length
- 642 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine--D-alanine ligase
- EC
- 6.3.2.4
- UniProt
- Q5SHZ3
- Ligands
- ATP
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 321 | 32% helix, 23% strand | Q5SHZ3 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.78 | 0.95 | 30 | ATP |
| 2 | 175 | 0.75 | 0.92 | 36 | ATP |
| 3 | 411 | 0.72 | 0.83 | 37 | empty |
| 4 | 425 | 0.70 | 0.81 | 37 | empty |
| 5 | 108 | 0.43 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1459 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 d-amino (D-amino acid).
Compared structures
- 2ZDQ · Crystal structure of D-Alanine:D-Alanine Ligase with ATP and D-Alanine:D-Alanine from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SHZ3 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (Q5SHZ3) · a predicted model of the same protein · chain B against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q5SHZ3
- Elsewhere: RCSB PDB 2ZDQ · PDBe 2ZDQ · UniProt Q5SHZ3
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