Research workbench
Heterodimer between H48F-YSOD1 and yccs
Analyse Heterodimer between H48F-YSOD1 and yccs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JK9
- Type
- protein
- Length
- 792 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase; Copper chaperone for superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- P00445, P40202
- Ligands
- ZN, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Superoxide dismutase (EC 1.15.1.1) | protein | 153 | 5% helix, 37% strand | P00445 |
| B, D | Copper chaperone for superoxide dismutase | protein | 243 | 16% helix, 40% strand | P40202 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.78 | 0.80 | 84 | empty |
| 2 | 1157 | 0.76 | 0.79 | 88 | empty |
| 3 | 424 | 0.76 | 0.85 | 46 | empty |
| 4 | 574 | 0.73 | 0.81 | 66 | SO4 |
| 5 | 380 | 0.72 | 0.84 | 39 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1207 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1112 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1093 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 640 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 582 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1JK9 · Heterodimer between H48F-ySOD1 and yCCS · the same entry in another collection · chain A against A, TM-score 1.00
- P00445 · AlphaFold monomer V2.0 prediction for superoxide dismutase [cu-zn] (P00445) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P40202 · AlphaFold monomer V2.0 prediction for superoxide dismutase 1 copper chaperone (P40202) · a predicted model of the same protein · chain B against A, TM-score 0.76
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 P00445
- Every structure of UniProt P40202
- Elsewhere: RCSB PDB 1JK9 · PDBe 1JK9 · UniProt P00445 · UniProt P40202
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