Research workbench
Crystal structure of D-alanine-D-alanine ligase from burkholderia xenovorans
Analyse Crystal structure of D-alanine-D-alanine ligase from burkholderia xenovorans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EGJ
- Type
- protein
- Length
- 1,099 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine--D-alanine ligase
- EC
- 6.3.2.4
- UniProt
- Q13TZ4
- Pockets
- 7 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 285 | 39% helix, 23% strand | Q13TZ4 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 285 | 39% helix, 24% strand | Q13TZ4 |
| C | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 283 | 38% helix, 23% strand | Q13TZ4 |
| D | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 246 | 37% helix, 23% strand | Q13TZ4 |
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.51 | 0.74 | 44 | empty |
| 2 | 179 | 0.45 | 0.75 | 40 | empty |
| 3 | 189 | 0.45 | 0.74 | 37 | empty |
| 4 | 104 | 0.43 | 0.78 | 25 | empty |
| 5 | 52 | 0.39 | 0.81 | 13 | empty |
Compared structures
- 4EGJ · Crystal structure of D-alanine-D-alanine ligase from Burkholderia xenovorans · the same entry in another collection · chain A against A, TM-score 1.00
- Q13TZ4 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (Q13TZ4) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q13TZ4
- Elsewhere: RCSB PDB 4EGJ · PDBe 4EGJ · UniProt Q13TZ4
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