Research workbench
Human apo-SOD1 bound to PTCL2(1R,2R-1,4-dach
Analyse Human apo-SOD1 bound to PTCL2(1R,2R-1,4-dach in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FFK
- Type
- protein
- Length
- 558 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
- D7Z
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 153 | 5% helix, 41% strand | P00441 |
| D, F | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 126 | 6% helix, 49% strand | P00441 |
Ligands and binding sites
- D7Z · PtCl2(1(R),2(R)-DACH) · ligand · 4 copies · chains A, B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.64 | 0.84 | 29 | empty |
| 2 | 181 | 0.61 | 0.83 | 32 | empty |
| 3 | 252 | 0.48 | 0.74 | 37 | empty |
| 4 | 124 | 0.35 | 0.72 | 23 | D7Z |
| 5 | 91 | 0.30 | 0.72 | 18 | D7Z |
Interfaces
4 interfaces between chains.
- D–F · 751 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 738 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 482 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 201 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6FFK · Human apo-SOD1 bound to PtCl2(1R,2R-1,4-DACH · 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 6FFK · PDBe 6FFK · UniProt P00441
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.