Research workbench
A designed pentameric membrane protein stabilized by van der waals interaction
Analyse A designed pentameric membrane protein stabilized by van der waals interaction in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MCT
- Type
- protein
- Length
- 390 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mini-evgl membrane protein
- Ligands
- NH2, SO4
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 92% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O | Mini-evgl membrane protein | protein | 26 | 92% helix, 0% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · 15 copies · chains A, B, C, D, E, K, F, G, H, I, J, L, M, N, O
- SO4 · Sulfate ion · ion · 8 copies · chains B, C, I, G, J, K, A, E, L
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 16 copies · chains A, B, C, D, E, K, L, F, G, H, I, J, M, N, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.76 | 0.93 | 25 | C8E |
| 2 | 505 | 0.67 | 0.77 | 43 | SO4, C8E |
| 3 | 75 | 0.62 | 0.88 | 15 | C8E |
| 4 | 65 | 0.59 | 0.88 | 15 | C8E |
| 5 | 83 | 0.59 | 0.86 | 15 | C8E |
Interfaces
25 interfaces between chains.
- L–M · 624 Ų buried · 0 hydrogen bonds · protein-protein
- K–L · 611 Ų buried · 0 hydrogen bonds · protein-protein
- F–J · 606 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 601 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 599 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6MCT · A designed pentameric membrane protein stabilized by van der Waals interaction · 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
- Elsewhere: RCSB PDB 6MCT · PDBe 6MCT
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