Research workbench
Thiol peroxidase from chromobacterium violaceum
Analyse Thiol peroxidase from chromobacterium violaceum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KEB
- Type
- protein
- Length
- 696 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable thiol peroxidase
- EC
- 1.11.1.-
- UniProt
- Q7NRS2
- Ligands
- CL, SO4
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Probable thiol peroxidase (EC 1.11.1.-) | protein | 175 | 25% helix, 27% strand | Q7NRS2 |
| B, C | Probable thiol peroxidase (EC 1.11.1.-) | protein | 173 | 24% helix, 27% strand | Q7NRS2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.83 | 0.85 | 103 | CL |
| 2 | 348 | 0.63 | 0.78 | 41 | CL |
| 3 | 57 | 0.32 | 0.77 | 19 | empty |
| 4 | 68 | 0.32 | 0.74 | 13 | empty |
| 5 | 59 | 0.30 | 0.75 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1023 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1022 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 761 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 315 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 119 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3KEB · Thiol peroxidase from Chromobacterium violaceum · 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 Q7NRS2
- Elsewhere: RCSB PDB 3KEB · PDBe 3KEB · UniProt Q7NRS2
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