Research workbench
Crystal structure of ni-containing superoxide dismutase with ni-ligation corresponding to the oxidized state
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
- 1Q0D
- Type
- protein
- Length
- 1,404 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [ni]
- EC
- 1.15.1.1
- UniProt
- P80734
- Ligands
- 3NI, SO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Superoxide dismutase [ni] (EC 1.15.1.1) | protein | 117 | 79% helix, 0% strand | P80734 |
Ligands and binding sites
- 3NI · Nickel (III) ion · metal · 12 copies · chains A, C, B, D, F, E, G, H, K, I, J, L
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, D, C, E, F, G, H, J, I, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.80 | 0.84 | 142 | SO4 |
| 2 | 789 | 0.80 | 0.83 | 150 | SO4 |
| 3 | 603 | 0.67 | 0.77 | 57 | SO4 |
| 4 | 106 | 0.57 | 0.85 | 30 | empty |
| 5 | 69 | 0.49 | 0.84 | 20 | empty |
Interfaces
26 interfaces between chains.
- J–L · 965 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 956 Ų buried · 13 hydrogen bonds · protein-protein
- G–I · 952 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 951 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 944 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1Q0D · Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to… · the same entry in another collection · chain L against L, 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 1Q0D · PDBe 1Q0D · UniProt P80734
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