MolNFT v1 · #153762 · protein
Crystal structure of a hypothetical fe superoxide dismutase
6JOV · Fe-superoxide dismutase: “Crystal structure of a hypothetical fe superoxide dismutase”. X-ray diffraction, 1 ligand (FE), 5 pockets (best druggability 0.69). MolNFT v1 #153762 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6JOV
- Type
- protein
- Length
- 790 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fe-superoxide dismutase
- EC
- 1.15.1.1
- Ligands
- FE
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fe-superoxide dismutase (EC 1.15.1.1) | protein | 197 | 55% helix, 13% strand | — |
| C, D | Fe-superoxide dismutase (EC 1.15.1.1) | protein | 198 | 57% helix, 13% strand | — |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 6 copies · chains A, B, C
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, D
- P6G · Hexaethylene glycol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.69 | 0.73 | 83 | PGE, PEG, EDO |
| 2 | 204 | 0.57 | 0.80 | 20 | PEG, EDO |
| 3 | 205 | 0.56 | 0.79 | 21 | EDO |
| 4 | 220 | 0.56 | 0.78 | 25 | EDO |
| 5 | 204 | 0.54 | 0.78 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 964 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 962 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 163 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 153 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 90 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6JOV · Crystal structure of a hypothetical Fe Superoxide dismutase · 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 6JOV · PDBe 6JOV
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