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
- 4DWZ
- Type
- protein
- Length
- 1,586 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein TON_0340
- UniProt
- B6YTD8
- Ligands
- ZN
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein TON_0340 | protein | 258 | 45% helix, 17% strand | B6YTD8 |
| B | Hypothetical protein TON_0340 | protein | 265 | 44% helix, 16% strand | B6YTD8 |
| C, D, F | Hypothetical protein TON_0340 | protein | 269 | 41% helix, 13% strand | B6YTD8 |
| E | Hypothetical protein TON_0340 | protein | 256 | 40% helix, 17% strand | B6YTD8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 38 copies · chains A, B, D, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.83 | 0.84 | 83 | ZN |
| 2 | 1064 | 0.81 | 0.82 | 91 | ZN |
| 3 | 922 | 0.81 | 0.82 | 80 | ZN |
| 4 | 87 | 0.72 | 0.95 | 20 | empty |
| 5 | 499 | 0.69 | 0.80 | 52 | empty |
Interfaces
9 interfaces between chains.
- C–E · 1298 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1282 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 1246 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 599 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 597 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4DWZ · 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 4DWZ · PDBe 4DWZ · UniProt B6YTD8
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