Research workbench
Crystal structure of dps protein from vibrio cholerae O1, a member of a broad superfamily of ferritin-like diiron-carboxylate proteins
Analyse Crystal structure of dps protein from vibrio cholerae O1, a member of a broad… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IQ1
- Type
- protein
- Length
- 631 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dps family protein
- UniProt
- Q9KVK4
- Ligands
- CL
- Pockets
- 5 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dps family protein | protein | 156 | 77% helix, 1% strand | Q9KVK4 |
| B, D | Dps family protein | protein | 159 | 75% helix, 1% strand | Q9KVK4 |
| C | Dps family protein | protein | 157 | 76% helix, 1% strand | Q9KVK4 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
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 | 94 | 0.40 | 0.77 | 17 | empty |
| 2 | 52 | 0.36 | 0.79 | 12 | empty |
| 3 | 54 | 0.35 | 0.78 | 13 | empty |
| 4 | 80 | 0.32 | 0.74 | 16 | empty |
| 5 | 76 | 0.32 | 0.74 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–D · 1333 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1327 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3IQ1 · Crystal structure of DPS protein from Vibrio cholerae O1, a member of a broad superfamily… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9KVK4
- Elsewhere: RCSB PDB 3IQ1 · PDBe 3IQ1 · UniProt Q9KVK4
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