Research workbench
Cambialistic superoxide dismutase from porphyromonas gingivalis
Analyse Cambialistic superoxide dismutase from porphyromonas gingivalis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QNN
- Type
- protein
- Length
- 763 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- P19665
- Ligands
- FE
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Superoxide dismutase (EC 1.15.1.1) | protein | 191 | 52% helix, 12% strand | P19665 |
| D | Superoxide dismutase (EC 1.15.1.1) | protein | 190 | 52% helix, 12% strand | P19665 |
Ligands and binding sites
- FE · Fe (III) 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
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.62 | 0.79 | 33 | empty |
| 2 | 373 | 0.61 | 0.77 | 51 | empty |
| 3 | 260 | 0.57 | 0.78 | 28 | empty |
| 4 | 192 | 0.56 | 0.80 | 20 | empty |
| 5 | 162 | 0.55 | 0.81 | 23 | empty |
Interfaces
5 interfaces between chains.
- C–D · 957 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 942 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 400 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 154 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 77 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1QNN · Cambialistic superoxide dismutase from Porphyromonas gingivalis · the same entry in another collection · chain A against A, TM-score 1.00
- P19665 · AlphaFold monomer V2.0 prediction for superoxide dismutase [MN/FE] (P19665) · a predicted model of the same protein · 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
- Every structure of UniProt P19665
- Elsewhere: RCSB PDB 1QNN · PDBe 1QNN · UniProt P19665
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