Research workbench
Crystal structure of superoxide reductase in the reduced state at 2.0 ångströms resolution
Analyse Crystal structure of superoxide reductase in the reduced state at 2.0 ångströms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DQK
- Type
- protein
- Length
- 496 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide reductase
- UniProt
- P82385
- Ligands
- FE2
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Superoxide reductase | protein | 124 | 3% helix, 53% strand | P82385 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.76 | 0.98 | 26 | empty |
| 2 | 81 | 0.75 | 0.98 | 24 | empty |
| 3 | 69 | 0.33 | 0.75 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1374 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1368 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1310 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1303 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 576 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1DQK · Crystal structure of superoxide reductase in the reduced state at 2.0 ångströms resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P82385 · AlphaFold monomer V2.0 prediction for superoxide reductase (P82385) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P82385
- Elsewhere: RCSB PDB 1DQK · PDBe 1DQK · UniProt P82385
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