Research workbench
C6A/C111A/C57A/C146A holo cuzn superoxide dismutase
Analyse C6A/C111A/C57A/C146A holo cuzn superoxide dismutase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GBV
- Type
- protein
- Length
- 1,530 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase [cu-zn]
- EC
- 1.15.1.1
- UniProt
- P00441
- Ligands
- CU1, ZN
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 153 | 6% helix, 39% strand | P00441 |
Ligands and binding sites
- CU1 · Copper (I) ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- ZN · Zinc ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.81 | 0.84 | 88 | empty |
| 2 | 1088 | 0.75 | 0.78 | 111 | empty |
| 3 | 843 | 0.73 | 0.78 | 80 | empty |
| 4 | 377 | 0.70 | 0.82 | 60 | empty |
| 5 | 133 | 0.67 | 0.89 | 26 | empty |
Interfaces
14 interfaces between chains.
- E–J · 737 Ų buried · 4 hydrogen bonds · protein-protein
- C–H · 728 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 720 Ų buried · 4 hydrogen bonds · protein-protein
- D–I · 717 Ų buried · 4 hydrogen bonds · protein-protein
- B–G · 714 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2GBV · C6A/C111A/C57A/C146A holo CuZn Superoxide dismutase · the same entry in another collection · chain E against E, 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 P00441
- Elsewhere: RCSB PDB 2GBV · PDBe 2GBV · UniProt P00441
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