Research workbench
Crystal structure of human cu-zn superoxide dismutase mutant G85R in space group I212121
Analyse Crystal structure of human cu-zn superoxide dismutase mutant G85R in space… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZKX
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- 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
- 5 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 153 | 6% helix, 41% strand | P00441 |
| B | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 152 | 7% helix, 40% strand | P00441 |
| C | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 151 | 3% helix, 40% strand | P00441 |
| D | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 118 | 3% helix, 50% strand | P00441 |
Ligands and binding sites
- CU1 · Copper (I) ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.75 | 0.78 | 105 | empty |
| 2 | 126 | 0.63 | 0.87 | 27 | empty |
| 3 | 182 | 0.58 | 0.82 | 29 | empty |
| 4 | 86 | 0.31 | 0.72 | 19 | empty |
| 5 | 71 | 0.28 | 0.72 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 766 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 590 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 421 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 349 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2ZKX · Crystal structure of human Cu-Zn superoxide dismutase mutant G85R in space group I212121 · the same entry in another collection · 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 P00441
- Elsewhere: RCSB PDB 2ZKX · PDBe 2ZKX · UniProt P00441
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