Research workbench
Human SOD1 G93A variant
Analyse Human SOD1 G93A variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GZO
- 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
- ACE, CU, ZN
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 40% 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 | 7% helix, 40% strand | P00441 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- CU · Copper (II) 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
- GOL · Glycerol · additive · 2 copies · chains B, J
- MLI · Malonate ion · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.81 | 0.82 | 113 | empty |
| 2 | 1097 | 0.78 | 0.80 | 108 | empty |
| 3 | 759 | 0.72 | 0.78 | 73 | empty |
| 4 | 261 | 0.65 | 0.83 | 40 | empty |
| 5 | 158 | 0.64 | 0.86 | 33 | empty |
Interfaces
13 interfaces between chains.
- G–H · 731 Ų buried · 4 hydrogen bonds · protein-protein
- I–J · 715 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 702 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 685 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 683 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent (covalent ligand).
Compared structures
- 3GZO · HUMAN SOD1 G93A Variant · 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 3GZO · PDBe 3GZO · UniProt P00441
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