MolNFT v1 · #62976 · protein
Crystal structure of the metal-bound superoxide dismutase from pyrobaculum aerophilum
3EVK · Superoxide dismutase [fe]: “Crystal structure of the metal-bound superoxide dismutase from pyrobaculum aerophilum”. X-ray diffraction, 1 ligand (MN), 11 pockets (best druggability 0.86). MolNFT v1 #62976 on GenesisL1: 3D structure…
- PDB
- 3EVK
- Type
- protein
- Length
- 844 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [fe]
- EC
- 1.15.1.1
- UniProt
- O93724
- Ligands
- MN
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Superoxide dismutase [fe] (EC 1.15.1.1) | protein | 211 | 50% helix, 14% strand | O93724 |
Ligands and binding sites
- MN · Manganese (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
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.86 | 0.95 | 36 | empty |
| 2 | 295 | 0.60 | 0.78 | 34 | empty |
| 3 | 311 | 0.59 | 0.77 | 33 | empty |
| 4 | 277 | 0.58 | 0.78 | 20 | empty |
| 5 | 303 | 0.57 | 0.77 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–D · 3039 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 3029 Ų buried · 51 hydrogen bonds · protein-protein
- B–D · 961 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 948 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 293 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3EVK · Crystal structure of the metal-bound superoxide dismutase from Pyrobaculum aerophilum · the same entry in another collection · chain A against A, TM-score 1.00
- O93724 · AlphaFold monomer V2.0 prediction for superoxide dismutase [fe] (O93724) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O93724
- Elsewhere: RCSB PDB 3EVK · PDBe 3EVK · UniProt O93724
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