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The crystal structure of the D-alanyl-alanine synthetase a from salmonella enterica typhimurium complexed with ADP
Analyse The crystal structure of the D-alanyl-alanine synthetase a from salmonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q1K
- Type
- protein
- Length
- 1,403 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine--D-alanine ligase a
- EC
- 6.3.2.4
- UniProt
- P0A1F0
- Ligands
- ADP, MG, SO4
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine--D-alanine ligase a (EC 6.3.2.4) | protein | 357 | 30% helix, 26% strand | P0A1F0 |
| B | D-alanine--D-alanine ligase a (EC 6.3.2.4) | protein | 346 | 30% helix, 27% strand | P0A1F0 |
| C | D-alanine--D-alanine ligase a (EC 6.3.2.4) | protein | 345 | 30% helix, 26% strand | P0A1F0 |
| D | D-alanine--D-alanine ligase a (EC 6.3.2.4) | protein | 355 | 30% helix, 26% strand | P0A1F0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, B, D
- SO4 · Sulfate ion · ion · chains B
- FMT · Formic acid · additive · 5 copies · chains A, B, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.85 | 0.86 | 103 | GOL, ADP, MG |
| 2 | 1036 | 0.83 | 0.84 | 105 | FMT |
| 3 | 881 | 0.82 | 0.84 | 77 | FMT, GOL |
| 4 | 1056 | 0.81 | 0.82 | 83 | FMT |
| 5 | 442 | 0.74 | 0.83 | 48 | ADP, MG |
Interfaces
4 interfaces between chains.
- A–B · 2334 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2309 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 690 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 107 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 3Q1K · The Crystal Structure of the D-alanyl-alanine Synthetase A from Salmonella enterica… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A1F0 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase a (P0A1F0) · a predicted model of the same protein · chain B 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 P0A1F0
- Elsewhere: RCSB PDB 3Q1K · PDBe 3Q1K · UniProt P0A1F0
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