MolNFT v1 · #135396 · protein
Structure of PFP1 protease from thermococcus thioreducens: large cell H3 crystal form
5TXW · Peptidase: “Structure of PFP1 protease from thermococcus thioreducens: large cell H3 crystal form”. X-ray diffraction, 6 pockets (best druggability 0.41). MolNFT v1 #135396 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5TXW
- Type
- protein
- Length
- 664 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase
- UniProt
- A0A0Q2XKL6
- Pockets
- 6 · best druggability 0.41
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidase | protein | 166 | 39% helix, 25% strand | A0A0Q2XKL6 |
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.41 | 0.72 | 19 | empty |
| 2 | 133 | 0.39 | 0.73 | 17 | empty |
| 3 | 116 | 0.38 | 0.74 | 21 | empty |
| 4 | 103 | 0.36 | 0.74 | 16 | empty |
| 5 | 111 | 0.36 | 0.73 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 879 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 875 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 125 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 116 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified, 2 disulfide (oxidation, disulfide).
Compared structures
- 5TXW · Structure of Pfp1 protease from Thermococcus thioreducens: large cell H3 crystal form · 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 A0A0Q2XKL6
- Elsewhere: RCSB PDB 5TXW · PDBe 5TXW · UniProt A0A0Q2XKL6
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