Research workbench
Contribution to structure and catalysis of tyrosine 34 in human manganese superoxide dismutase
Analyse Contribution to structure and catalysis of tyrosine 34 in human manganese… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P4K
- 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
- 10 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Superoxide dismutase (EC 1.15.1.1) | protein | 198 | 59% 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
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.55 | 0.80 | 21 | empty |
| 2 | 196 | 0.55 | 0.79 | 23 | empty |
| 3 | 202 | 0.55 | 0.79 | 22 | empty |
| 4 | 208 | 0.54 | 0.78 | 22 | empty |
| 5 | 250 | 0.50 | 0.74 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 984 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 970 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 928 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 918 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 340 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2P4K · Contribution to Structure and Catalysis of Tyrosine 34 in Human Manganese Superoxide… · 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 2P4K · PDBe 2P4K · UniProt P04179
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