MolNFT v1 · #76590 · protein
Crystal structure of peroxiredoxin PRX4 from pseudosciaena crocea
3QPM: “Crystal structure of peroxiredoxin PRX4 from pseudosciaena crocea”. X-ray diffraction, 13 pockets (best druggability 0.74). MolNFT v1 #76590 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3QPM
- Type
- protein
- Length
- 974 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxiredoxin
- EC
- 1.11.1.15
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxiredoxin (EC 1.11.1.15) | protein | 195 | 30% helix, 27% strand | — |
| B, C | Peroxiredoxin (EC 1.11.1.15) | protein | 194 | 30% helix, 27% strand | — |
| D | Peroxiredoxin (EC 1.11.1.15) | protein | 196 | 30% helix, 27% strand | — |
| E | Peroxiredoxin (EC 1.11.1.15) | protein | 195 | 30% helix, 25% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B, D, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.74 | 0.98 | 23 | empty |
| 2 | 58 | 0.71 | 0.98 | 21 | empty |
| 3 | 283 | 0.66 | 0.82 | 45 | empty |
| 4 | 161 | 0.65 | 0.86 | 31 | empty |
| 5 | 226 | 0.59 | 0.80 | 29 | GOL |
Interfaces
7 interfaces between chains.
- A–B · 2334 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2325 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 674 Ų buried · 0 hydrogen bonds · protein-protein
- C–E · 666 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 61 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3QPM · Crystal structure of peroxiredoxin Prx4 from Pseudosciaena crocea · 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
- Elsewhere: RCSB PDB 3QPM · PDBe 3QPM
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