Research workbench
Structure of the pyrococcus furiosus esterase PF2001 with space group P212121
Analyse Structure of the pyrococcus furiosus esterase PF2001 with space group P212121 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LCN
- Type
- protein
- Length
- 1,063 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q8TZJ1
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 268 | 37% helix, 22% strand | Q8TZJ1 |
| B | Uncharacterized protein | protein | 262 | 39% helix, 21% strand | Q8TZJ1 |
| C | Uncharacterized protein | protein | 265 | 41% helix, 22% strand | Q8TZJ1 |
| D | Uncharacterized protein | protein | 268 | 37% helix, 20% strand | Q8TZJ1 |
Ligands and binding sites
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.86 | 0.97 | 26 | empty |
| 2 | 1177 | 0.83 | 0.84 | 145 | 1PE |
| 3 | 403 | 0.82 | 0.90 | 63 | 1PE |
| 4 | 303 | 0.80 | 0.91 | 35 | empty |
| 5 | 73 | 0.71 | 0.96 | 23 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1982 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1809 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 438 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 400 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 319 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5LCN · Structure of the pyrococcus furiosus esterase PF2001 with space group P212121 · 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 Q8TZJ1
- Elsewhere: RCSB PDB 5LCN · PDBe 5LCN · UniProt Q8TZJ1
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