Research workbench
Crystal structure of acylphosphatase C20R mutant from vibrio CHOLERAE0395
Analyse Crystal structure of acylphosphatase C20R mutant from vibrio CHOLERAE0395 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HI1
- Type
- protein
- Length
- 259 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acylphosphatase
- EC
- 3.6.1.7
- UniProt
- A5F8G9
- Ligands
- MOO, SO4
- Pockets
- 5 · best druggability 0.35
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acylphosphatase (EC 3.6.1.7) | protein | 88 | 27% helix, 36% strand | A5F8G9 |
| B | Acylphosphatase (EC 3.6.1.7) | protein | 84 | 29% helix, 39% strand | A5F8G9 |
| C | Acylphosphatase (EC 3.6.1.7) | protein | 87 | 28% helix, 34% strand | A5F8G9 |
Ligands and binding sites
- MOO · Molybdate ion · ion · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.35 | 0.77 | 16 | MOO |
| 2 | 103 | 0.35 | 0.74 | 25 | SO4 |
| 3 | 63 | 0.34 | 0.77 | 15 | MOO |
| 4 | 89 | 0.32 | 0.73 | 18 | empty |
| 5 | 50 | 0.31 | 0.77 | 16 | MOO |
Interfaces
3 interfaces between chains.
- B–C · 349 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 341 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 340 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4HI1 · Crystal structure of acylphosphatase C20R mutant from Vibrio cholerae0395 · the same entry in another collection · chain A against A, TM-score 1.00
- A5F8G9 · AlphaFold monomer V2.0 prediction for acylphosphatase (A5F8G9) · 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 A5F8G9
- Elsewhere: RCSB PDB 4HI1 · PDBe 4HI1 · UniProt A5F8G9
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