MolNFT v1 · #124019 · protein
Crystal structure of reduced PRX3 in complex with H2O2 from vibrio vulnificus
5K2J · 1-cys peroxiredoxin: “Crystal structure of reduced PRX3 in complex with H2O2 from vibrio vulnificus”. X-ray diffraction, 1 ligand (PEO), 20 pockets (best druggability 0.68). MolNFT v1 #124019 on GenesisL1: 3D structure, binding…
- 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
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