MolNFT v1 · #47639 · protein
Contribution to structure and catalysis of tyrosine 34 in human manganese superoxide dismutase
2P4K: “Contribution to structure and catalysis of tyrosine 34 in human manganese superoxide dismutase”. X-ray diffraction, 1 ligand (MN), 10 pockets (best druggability 0.55). MolNFT v1 #47639 on GenesisL1: 3D structure, binding sites and…
- 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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