MolNFT v1 · #106320 · protein
Crystal structure of superoxide dismutase from sedum alfredii
4RVP: “Crystal structure of superoxide dismutase from sedum alfredii”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.79). MolNFT v1 #106320 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4RVP
- Type
- protein
- Length
- 923 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase
- EC
- 1.15.1.1
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F | Superoxide dismutase (EC 1.15.1.1) | protein | 153 | 5% helix, 39% strand | — |
| D | Superoxide dismutase (EC 1.15.1.1) | protein | 158 | 3% helix, 40% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.79 | 0.81 | 105 | empty |
| 2 | 512 | 0.69 | 0.79 | 55 | empty |
| 3 | 174 | 0.61 | 0.83 | 26 | empty |
| 4 | 188 | 0.46 | 0.75 | 26 | empty |
| 5 | 164 | 0.42 | 0.74 | 28 | empty |
Interfaces
8 interfaces between chains.
- C–D · 702 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 667 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 411 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 400 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 335 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4RVP · Crystal structure of superoxide dismutase from sedum alfredii · 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
- Elsewhere: RCSB PDB 4RVP · PDBe 4RVP
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