MolNFT v1 · #51885 · protein
Structure of the soluble domain of the membrane protein TM1634 from thermotoga maritima
2VKO: “Structure of the soluble domain of the membrane protein TM1634 from thermotoga maritima”. X-ray diffraction, 5 pockets (best druggability 0.62). MolNFT v1 #51885 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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
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