Research workbench
Crystal structure of ni-containing superoxide dismutase with ni-ligation corresponding to the state after full X- ray-induced reduction
Analyse Crystal structure of ni-containing superoxide dismutase with ni-ligation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q0M
- Type
- protein
- Length
- 702 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [ni]
- EC
- 1.15.1.1
- UniProt
- P80734
- Ligands
- NI, SO4
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Superoxide dismutase [ni] (EC 1.15.1.1) | protein | 117 | 78% helix, 0% strand | P80734 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 6 copies · chains A, B, C, D, F, E
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, E, F, D
- ACY · Acetic acid · additive · 3 copies · chains C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.80 | 0.83 | 141 | SO4 |
| 2 | 77 | 0.56 | 0.87 | 31 | empty |
| 3 | 60 | 0.29 | 0.74 | 15 | SO4 |
Interfaces
12 interfaces between chains.
- D–F · 997 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 942 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 933 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 864 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 861 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1Q0M · Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to… · the same entry in another collection · chain C against C, TM-score 1.00
- P80734 · AlphaFold monomer V2.0 prediction for superoxide dismutase [ni] (P80734) · 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 P80734
- Elsewhere: RCSB PDB 1Q0M · PDBe 1Q0M · UniProt P80734
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