MolNFT v1 · #186212 · protein
Structure of PFP1 protease from thermococcus thioreducens: large unit cell at 1.44 a resolution
7R66 · Peptidase: “Structure of PFP1 protease from thermococcus thioreducens: large unit cell at 1.44 a resolution”. X-ray diffraction, 1 ligand (PO4), 5 pockets (best druggability 0.44). MolNFT v1 #186212 on GenesisL1: 3D structure…
- PDB
- 7R66
- Type
- protein
- Length
- 664 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase
- UniProt
- A0A0Q2XKL6
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.44
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 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.44 | 0.73 | 22 | empty |
| 2 | 178 | 0.43 | 0.73 | 18 | empty |
| 3 | 134 | 0.40 | 0.74 | 18 | MPD |
| 4 | 131 | 0.39 | 0.73 | 17 | MPD |
| 5 | 77 | 0.29 | 0.73 | 13 | empty |
Interfaces
4 interfaces between chains.
- C–D · 898 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 897 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 144 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 134 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified, 2 disulfide (oxidation, disulfide).
Compared structures
- 7R66 · Structure of Pfp1 protease from Thermococcus thioreducens: large unit cell at 1.44 A… · 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 7R66 · PDBe 7R66 · UniProt A0A0Q2XKL6
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