Research workbench
Crystal structure of human peroxiredoxin 4(THIOREDOXIN peroxidase) with mesna
Analyse Crystal structure of human peroxiredoxin 4(THIOREDOXIN peroxidase) with mesna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RQX
- Type
- protein
- Length
- 830 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxiredoxin-4
- EC
- 1.11.1.15
- UniProt
- Q13162
- Ligands
- COM
- Pockets
- 11 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Peroxiredoxin-4 (EC 1.11.1.15) | protein | 166 | 30% helix, 28% strand | Q13162 |
Ligands and binding sites
- COM · 1-thioethanesulfonic acid · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.53 | 0.76 | 33 | empty |
| 2 | 210 | 0.51 | 0.76 | 30 | empty |
| 3 | 171 | 0.49 | 0.77 | 36 | empty |
| 4 | 79 | 0.45 | 0.81 | 19 | empty |
| 5 | 94 | 0.43 | 0.78 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 914 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 886 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 779 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 757 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 4RQX · Crystal structure of human peroxiredoxin 4(THIOREDOXIN PEROXIDASE) with MESNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q13162 · AlphaFold monomer V2.0 prediction for peroxiredoxin-4 (Q13162) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q13162
- Elsewhere: RCSB PDB 4RQX · PDBe 4RQX · UniProt Q13162
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