Research workbench
Human SOD1 H80R variant, P212121 crystal form
Analyse Human SOD1 H80R variant, P212121 crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QQD
- Type
- protein
- Length
- 251 residues
- Chains
- 2
- 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
- ACE, ZN, SO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 123 | 7% helix, 49% strand | P00441 |
| B | Superoxide dismutase [cu-zn] (EC 1.15.1.1) | protein | 128 | 3% helix, 47% strand | P00441 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.63 | 0.85 | 31 | empty |
| 2 | 80 | 0.32 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 715 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (oxidation, covalent ligand).
Compared structures
- 3QQD · Human SOD1 H80R variant, P212121 crystal form · 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 3QQD · PDBe 3QQD · UniProt P00441
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