Research workbench
Allosteric inhibition of staphylococcus aureus D-ALANINE:D-alanine ligase revealed by crystallographic studies
Analyse Allosteric inhibition of staphylococcus aureus D-ALANINE:D-alanine ligase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I8C
- Type
- protein
- Length
- 692 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
- ADP, MG, SO4
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-alanine-D-alanine ligase (EC 6.3.2.4) | protein | 345 | 38% helix, 24% strand | Q5HEB7 |
| B | D-alanine-D-alanine ligase (EC 6.3.2.4) | protein | 347 | 37% helix, 22% strand | Q5HEB7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.83 | 0.84 | 118 | SO4 |
| 2 | 616 | 0.81 | 0.86 | 57 | empty |
| 3 | 727 | 0.74 | 0.80 | 72 | SO4, MG, ADP |
| 4 | 94 | 0.57 | 0.86 | 21 | empty |
| 5 | 161 | 0.47 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2525 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 2I8C · Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by… · 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 B against A, TM-score 0.96
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 2I8C · PDBe 2I8C · UniProt Q5HEB7
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