Research workbench
Structure of the D-alanine-D-alanine ligase from coxiella burnetii
Analyse Structure of the D-alanine-D-alanine ligase from coxiella burnetii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TQT
- Type
- protein
- Length
- 685 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
- Q83BZ9
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 348 | 38% helix, 25% strand | Q83BZ9 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 337 | 38% helix, 25% strand | Q83BZ9 |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 753 | 0.79 | 0.83 | 72 | empty |
| 2 | 642 | 0.78 | 0.84 | 66 | empty |
| 3 | 510 | 0.67 | 0.78 | 52 | empty |
| 4 | 360 | 0.63 | 0.78 | 48 | empty |
| 5 | 66 | 0.33 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2396 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3TQT · Structure of the D-alanine-D-alanine ligase from Coxiella burnetii · the same entry in another collection · chain A against A, TM-score 1.00
- Q83BZ9 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (Q83BZ9) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q83BZ9
- Elsewhere: RCSB PDB 3TQT · PDBe 3TQT · UniProt Q83BZ9
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