MolNFT v1 · #54456 · protein
Reduced thiol peroxidase (tpx) from yersinia pseudotuberculosis
2XPD: “Reduced thiol peroxidase (tpx) from yersinia pseudotuberculosis”. X-ray diffraction, 7 pockets (best druggability 0.84). MolNFT v1 #54456 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2XPD
- Type
- protein
- Length
- 1,002 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiol peroxidase
- EC
- 1.11.1.15
- UniProt
- Q66A71
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiol peroxidase (EC 1.11.1.15) | protein | 166 | 23% helix, 31% strand | Q66A71 |
| B, D, E | Thiol peroxidase (EC 1.11.1.15) | protein | 167 | 25% helix, 31% strand | Q66A71 |
| C | Thiol peroxidase (EC 1.11.1.15) | protein | 170 | 24% helix, 31% strand | Q66A71 |
| F | Thiol peroxidase (EC 1.11.1.15) | protein | 165 | 21% helix, 32% strand | Q66A71 |
Ligands and binding sites
- DTU · (2R,3S)-1,4-dimercaptobutane-2,3-diol · additive · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.84 | 0.85 | 127 | DTU |
| 2 | 1137 | 0.81 | 0.82 | 116 | empty |
| 3 | 124 | 0.49 | 0.80 | 23 | empty |
| 4 | 121 | 0.46 | 0.78 | 16 | empty |
| 5 | 66 | 0.42 | 0.81 | 16 | empty |
Interfaces
10 interfaces between chains.
- C–D · 775 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 738 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 736 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 387 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 373 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2XPD · Reduced Thiol peroxidase (Tpx) from yersinia Pseudotuberculosis · 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
- Every structure of UniProt Q66A71
- Elsewhere: RCSB PDB 2XPD · PDBe 2XPD · UniProt Q66A71
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