Research workbench
Crystal structure of S. aureus D-alanine alanyl carrier protein ligase
Analyse Crystal structure of S. aureus D-alanine alanyl carrier protein ligase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VHV
- Type
- protein
- Length
- 1,930 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-alanine--D-alanyl carrier protein ligase
- EC
- 6.2.1.54
- UniProt
- P68876
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, C | D-alanine--D-alanyl carrier protein ligase (EC 6.2.1.54) | protein | 480 | 34% helix, 27% strand | P68876 |
| A, B | D-alanine--D-alanyl carrier protein ligase (EC 6.2.1.54) | protein | 485 | 34% helix, 28% strand | P68876 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains D, C, A, B
- MG · Magnesium ion · metal · 4 copies · chains D, C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.83 | 0.84 | 101 | MG, ATP |
| 2 | 984 | 0.82 | 0.83 | 104 | MG, ATP |
| 3 | 556 | 0.81 | 0.87 | 72 | MG, ATP |
| 4 | 738 | 0.79 | 0.83 | 84 | MG, ATP |
| 5 | 788 | 0.70 | 0.76 | 84 | empty |
Interfaces
5 interfaces between chains.
- C–A · 615 Ų buried · 9 hydrogen bonds · protein-protein
- D–B · 340 Ų buried · 0 hydrogen bonds · protein-protein
- D–A · 305 Ų buried · 1 hydrogen bond · protein-protein
- C–B · 266 Ų buried · 3 hydrogen bonds · protein-protein
- D–C · 200 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7VHV · Crystal structure of S. aureus D-alanine alanyl carrier protein ligase · the same entry in another collection · chain B against B, TM-score 1.00
- P68876 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanyl carrier protein ligase (P68876) · a predicted model of the same protein · chain C against A, TM-score 0.81
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 P68876
- Elsewhere: RCSB PDB 7VHV · PDBe 7VHV · UniProt P68876
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