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Crystal structure of D-alanine-D-alanine ligase from acinetobacter baumannii, space group P212121
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
- 5DMX
- Type
- protein
- Length
- 1,460 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
- 17 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 234 | 37% helix, 21% strand | B2I1J3 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 259 | 34% helix, 23% strand | B2I1J3 |
| C | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 253 | 35% helix, 21% strand | B2I1J3 |
| D | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 276 | 33% helix, 21% strand | B2I1J3 |
| E | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 197 | 39% helix, 12% strand | B2I1J3 |
| F | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 241 | 39% helix, 20% strand | B2I1J3 |
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.74 | 0.97 | 25 | empty |
| 2 | 936 | 0.68 | 0.73 | 75 | empty |
| 3 | 305 | 0.62 | 0.79 | 44 | empty |
| 4 | 415 | 0.58 | 0.74 | 54 | empty |
| 5 | 112 | 0.51 | 0.82 | 29 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1226 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1199 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1189 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 583 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 253 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5DMX · Crystal structure of D-alanine-D-alanine ligase from Acinetobacter baumannii, space group… · 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 5DMX · PDBe 5DMX · UniProt B2I1J3
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