MolNFT v1 · #139306 · protein
Peroxiredoxin from pyrococcus horikoshii (6M mutant)
5XBQ: “Peroxiredoxin from pyrococcus horikoshii (6M mutant)”. X-ray diffraction, 20 pockets (best druggability 0.73). MolNFT v1 #139306 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XBQ
- Type
- protein
- Length
- 2,568 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxiredoxin
- EC
- 1.11.1.15
- UniProt
- O58966
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Peroxiredoxin (EC 1.11.1.15) | protein | 214 | 33% helix, 26% strand | O58966 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.73 | 0.77 | 63 | empty |
| 2 | 818 | 0.71 | 0.76 | 74 | empty |
| 3 | 777 | 0.70 | 0.77 | 65 | empty |
| 4 | 689 | 0.69 | 0.77 | 67 | empty |
| 5 | 723 | 0.68 | 0.76 | 67 | empty |
Interfaces
24 interfaces between chains.
- C–D · 2507 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 2474 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2471 Ų buried · 33 hydrogen bonds · protein-protein
- I–J · 2454 Ų buried · 36 hydrogen bonds · protein-protein
- K–L · 2451 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 12 modified (disulfide, oxidation).
Compared structures
- 5XBQ · Peroxiredoxin from Pyrococcus horikoshii (6m mutant) · the same entry in another collection · chain L against L, 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 O58966
- Elsewhere: RCSB PDB 5XBQ · PDBe 5XBQ · UniProt O58966
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