Research workbench
Crystal structure of reduced PRX3 in complex with H2O2 from vibrio vulnificus
Analyse Crystal structure of reduced PRX3 in complex with H2O2 from vibrio vulnificus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K2J
- Type
- protein
- Length
- 1,897 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-cys peroxiredoxin
- Ligands
- PEO
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 10 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-cys peroxiredoxin | protein | 160 | 34% helix, 28% strand | — |
| B, C | 1-cys peroxiredoxin | protein | 160 | 29% helix, 31% strand | — |
| D | 1-cys peroxiredoxin | protein | 159 | 32% helix, 28% strand | — |
| E | 1-cys peroxiredoxin | protein | 155 | 32% helix, 29% strand | — |
| F | 1-cys peroxiredoxin | protein | 161 | 30% helix, 29% strand | — |
| G, K | 1-cys peroxiredoxin | protein | 153 | 32% helix, 29% strand | — |
| H | 1-cys peroxiredoxin | protein | 158 | 29% helix, 31% strand | — |
| I | 1-cys peroxiredoxin | protein | 157 | 34% helix, 29% strand | — |
| J | 1-cys peroxiredoxin | protein | 157 | 29% helix, 31% strand | — |
| L | 1-cys peroxiredoxin | protein | 164 | 29% helix, 30% strand | — |
Ligands and binding sites
- PEO · Hydrogen peroxide · ligand · 4 copies · chains A, E, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.68 | 0.77 | 47 | PEO |
| 2 | 505 | 0.65 | 0.77 | 40 | empty |
| 3 | 569 | 0.64 | 0.75 | 46 | PEO |
| 4 | 533 | 0.64 | 0.76 | 37 | empty |
| 5 | 142 | 0.57 | 0.83 | 22 | empty |
Interfaces
16 interfaces between chains.
- I–J · 751 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 744 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 735 Ų buried · 3 hydrogen bonds · protein-protein
- G–H · 733 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 713 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5K2J · Crystal structure of reduced Prx3 in complex with h2o2 from Vibrio vulnificus · 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 5K2J · PDBe 5K2J
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.