MolNFT v1 · #50253 · protein
Crystal structure of the bacillus subtilis superoxide dismutase
2RCV · Superoxide dismutase [mn]: “Crystal structure of the bacillus subtilis superoxide dismutase”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.72). MolNFT v1 #50253 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2RCV
- Type
- protein
- Length
- 1,591 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [mn]
- EC
- 1.15.1.1
- UniProt
- P54375
- Ligands
- MN
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F, G | Superoxide dismutase [mn] (EC 1.15.1.1) | protein | 200 | 54% helix, 13% strand | P54375 |
| B, H | Superoxide dismutase [mn] (EC 1.15.1.1) | protein | 197 | 54% helix, 13% strand | P54375 |
| D | Superoxide dismutase [mn] (EC 1.15.1.1) | protein | 197 | 53% helix, 13% strand | P54375 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 746 | 0.72 | 0.78 | 67 | empty |
| 2 | 671 | 0.71 | 0.78 | 72 | empty |
| 3 | 402 | 0.57 | 0.74 | 42 | empty |
| 4 | 328 | 0.54 | 0.74 | 40 | empty |
| 5 | 175 | 0.53 | 0.79 | 21 | empty |
Interfaces
16 interfaces between chains.
- A–B · 910 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 908 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 906 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 902 Ų buried · 13 hydrogen bonds · protein-protein
- D–G · 225 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2RCV · Crystal structure of the Bacillus subtilis superoxide dismutase · the same entry in another collection · chain H against H, TM-score 1.00
- P54375 · AlphaFold monomer V2.0 prediction for superoxide dismutase [mn] (P54375) · a predicted model of the same protein · chain B 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 P54375
- Elsewhere: RCSB PDB 2RCV · PDBe 2RCV · UniProt P54375
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