Research workbench
Crystal structure of staphylococcus aureus vrsa-9 D-ALA:D-ala ligase
Analyse Crystal structure of staphylococcus aureus vrsa-9 D-ALA:D-ala ligase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N8D
- Type
- protein
- Length
- 663 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
- Q5HEB7
- Ligands
- ANP, SO4, CL
- Pockets
- 6 · best druggability 0.85
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 | 329 | 38% helix, 23% strand | Q5HEB7 |
| B | D-alanine--D-alanine ligase (EC 6.3.2.4) | protein | 334 | 40% helix, 23% strand | Q5HEB7 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.85 | 0.86 | 113 | ANP, SO4 |
| 2 | 1050 | 0.78 | 0.80 | 85 | SO4 |
| 3 | 82 | 0.48 | 0.82 | 16 | empty |
| 4 | 147 | 0.46 | 0.76 | 26 | ANP |
| 5 | 125 | 0.45 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2015 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3N8D · Crystal structure of Staphylococcus aureus VRSA-9 D-Ala:D-Ala ligase · the same entry in another collection · chain A against A, TM-score 1.00
- Q5HEB7 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (Q5HEB7) · 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 Q5HEB7
- Elsewhere: RCSB PDB 3N8D · PDBe 3N8D · UniProt Q5HEB7
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