Research workbench
Crystal structure of D-alanine-D-alanine ligase from acinetobacter baumannii
Analyse Crystal structure of D-alanine-D-alanine ligase from acinetobacter baumannii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D8D
- Type
- protein
- Length
- 1,676 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine--D-alanine ligase
- EC
- 6.3.2.4
- UniProt
- B2I1J3
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 282 | 37% helix, 22% strand | B2I1J3 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 282 | 36% helix, 22% strand | B2I1J3 |
| C | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 274 | 37% helix, 20% strand | B2I1J3 |
| D | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 284 | 36% helix, 22% strand | B2I1J3 |
| E | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 276 | 36% helix, 21% strand | B2I1J3 |
| F | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 278 | 38% helix, 19% strand | B2I1J3 |
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.73 | 0.76 | 133 | empty |
| 2 | 317 | 0.65 | 0.81 | 48 | empty |
| 3 | 331 | 0.63 | 0.79 | 42 | empty |
| 4 | 299 | 0.60 | 0.79 | 39 | empty |
| 5 | 274 | 0.60 | 0.79 | 40 | empty |
Interfaces
5 interfaces between chains.
- B–E · 1404 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1223 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1182 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 421 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 351 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5D8D · Crystal structure of D-alanine-D-alanine ligase from Acinetobacter baumannii · the same entry in another collection · chain F against F, TM-score 1.00
- B2I1J3 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (B2I1J3) · a predicted model of the same protein · chain D 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 B2I1J3
- Elsewhere: RCSB PDB 5D8D · PDBe 5D8D · UniProt B2I1J3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.