Research workbench
Interrupting the hydrogen bonding network at the active site of human manganese superoxide dismutase
Analyse Interrupting the hydrogen bonding network at the active site of human manganese… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GDS
- Type
- protein
- Length
- 792 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superoxide dismutase
- EC
- 1.15.1.1
- UniProt
- P04179
- Ligands
- MN
- Pockets
- 11 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Superoxide dismutase (EC 1.15.1.1) | protein | 198 | 58% helix, 13% strand | P04179 |
Ligands and binding sites
- MN · Manganese (II) 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
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.53 | 0.78 | 21 | empty |
| 2 | 180 | 0.53 | 0.79 | 22 | empty |
| 3 | 191 | 0.53 | 0.78 | 22 | empty |
| 4 | 191 | 0.52 | 0.78 | 21 | empty |
| 5 | 222 | 0.46 | 0.73 | 33 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1015 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 976 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 904 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 898 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 315 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2GDS · Interrupting the Hydrogen Bonding Network at the Active Site of Human Manganese… · the same entry in another collection · chain A against A, TM-score 1.00
- P04179 · AlphaFold monomer V2.0 prediction for superoxide dismutase [mn], mitochondrial (P04179) · a predicted model of the same protein · 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 P04179
- Elsewhere: RCSB PDB 2GDS · PDBe 2GDS · UniProt P04179
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