Research workbench
Structure of the soluble domain of the membrane protein TM1634 from thermotoga maritima
Analyse Structure of the soluble domain of the membrane protein TM1634 from thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VKO
- Type
- protein
- Length
- 413 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TM1634
- UniProt
- Q9X1W9
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TM1634 | protein | 104 | 80% helix, 0% strand | Q9X1W9 |
| B | TM1634 | protein | 103 | 82% helix, 0% strand | Q9X1W9 |
| C, D | TM1634 | protein | 103 | 83% helix, 0% strand | Q9X1W9 |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · chains A, C
- P6G · Hexaethylene glycol · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.62 | 0.79 | 29 | P6G |
| 2 | 330 | 0.61 | 0.77 | 34 | PG4 |
| 3 | 51 | 0.34 | 0.78 | 12 | empty |
| 4 | 54 | 0.29 | 0.75 | 12 | empty |
| 5 | 50 | 0.28 | 0.74 | 10 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1279 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1221 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 354 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2VKO · Structure of the soluble domain of the membrane protein TM1634 from Thermotoga maritima · 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 Q9X1W9
- Elsewhere: RCSB PDB 2VKO · PDBe 2VKO · UniProt Q9X1W9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.