MolNFT v1 · #4522 · protein
Crystal structure of superoxide reductase in the reduced state at 2.0 ångströms resolution
1DQK: “Crystal structure of superoxide reductase in the reduced state at 2.0 ångströms resolution”. X-ray diffraction, 1 ligand (FE2), 3 pockets (best druggability 0.76). MolNFT v1 #4522 on GenesisL1: 3D structure, binding sites and…
- 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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