MolNFT v1 · #1239 · protein
The cambialistic superoxide dismutase (fe-sod) of P. shermanii coordinated by azide
1AVM: “The cambialistic superoxide dismutase (fe-sod) of P. shermanii coordinated by azide”. X-ray diffraction, 2 ligands (FE, AZI), 4 pockets (best druggability 0.51). MolNFT v1 #1239 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1AVM
- Type
- protein
- Length
- 402 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- P80293
- Ligands
- FE, AZI
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Superoxide dismutase (EC 1.15.1.1) | protein | 201 | 54% helix, 13% strand | P80293 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.51 | 0.78 | 24 | empty |
| 2 | 173 | 0.51 | 0.78 | 25 | empty |
| 3 | 56 | 0.29 | 0.74 | 15 | empty |
| 4 | 51 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1042 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1AVM · The cambialistic superoxide dismutase (fe-sod) of P. shermanii coordinated by azide · the same entry in another collection · chain A against A, TM-score 1.00
- P80293 · AlphaFold monomer V2.0 prediction for superoxide dismutase [MN/FE] (P80293) · 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 P80293
- Elsewhere: RCSB PDB 1AVM · PDBe 1AVM · UniProt P80293
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