Research workbench
Crystal Structure of Ton_0340
Analyse Crystal Structure of Ton_0340 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FC5
- Type
- protein
- Length
- 1,591 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Thermococcus onnurineus
- Molecule
- Putative uncharacterized protein
- UniProt
- B6YTD8
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.3 · 4 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein | protein | 259 | 45% helix, 16% strand | B6YTD8 |
| B, D | Putative uncharacterized protein | protein | 268 | 45% helix, 16% strand | B6YTD8 |
| C, F | Putative uncharacterized protein | protein | 269 | 42% helix, 16% strand | B6YTD8 |
| E | Putative uncharacterized protein | protein | 258 | 45% helix, 17% strand | B6YTD8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 53 copies · chains A, D, B, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.85 | 0.85 | 113 | ZN |
| 2 | 1170 | 0.82 | 0.83 | 107 | ZN |
| 3 | 649 | 0.81 | 0.85 | 65 | ZN |
| 4 | 337 | 0.69 | 0.82 | 43 | empty |
| 5 | 334 | 0.60 | 0.77 | 44 | ZN |
Interfaces
9 interfaces between chains.
- B–D · 1332 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 1269 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 1252 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 570 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 563 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4FC5 · Crystal structure of TON_0340 · 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 B6YTD8
- Elsewhere: RCSB PDB 4FC5 · PDBe 4FC5 · UniProt B6YTD8
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