Research workbench
Crystal structure of D-alanine--D-alanine ligase from burkholderia ambifaria
Analyse Crystal structure of D-alanine--D-alanine ligase from burkholderia ambifaria in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EG0
- Type
- protein
- Length
- 579 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
- B1YSS6
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 288 | 39% helix, 23% strand | B1YSS6 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 291 | 39% helix, 23% strand | B1YSS6 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.48 | 0.74 | 44 | EDO |
| 2 | 147 | 0.46 | 0.77 | 33 | EDO |
| 3 | 148 | 0.40 | 0.74 | 21 | empty |
| 4 | 75 | 0.32 | 0.74 | 22 | empty |
| 5 | 81 | 0.31 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1136 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4EG0 · Crystal Structure of D-alanine--D-alanine ligase from Burkholderia ambifaria · the same entry in another collection · chain A against A, TM-score 1.00
- B1YSS6 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (B1YSS6) · 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 B1YSS6
- Elsewhere: RCSB PDB 4EG0 · PDBe 4EG0 · UniProt B1YSS6
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