Research workbench
Crystal structure of a membrane protein
Analyse Crystal structure of a membrane protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UDC
- Type
- protein
- Length
- 1,869 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small-conductance mechanosensitive channel, C-terminal peptide from small-conductance…
- UniProt
- Q8R6L9, P0C0S1
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Small-conductance mechanosensitive channel, C-terminal peptide from small-conductance mechanosensitive channel | protein | 267 | 50% helix, 24% strand | Q8R6L9, P0C0S1 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.79 | 0.80 | 56 | empty |
| 2 | 830 | 0.69 | 0.74 | 71 | empty |
| 3 | 727 | 0.67 | 0.74 | 72 | empty |
| 4 | 582 | 0.66 | 0.76 | 45 | empty |
| 5 | 571 | 0.66 | 0.76 | 40 | empty |
Interfaces
14 interfaces between chains.
- E–F · 3137 Ų buried · 28 hydrogen bonds · protein-protein
- C–F · 3128 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 3127 Ų buried · 29 hydrogen bonds · protein-protein
- C–G · 3116 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 3109 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 3UDC · Crystal structure of a membrane protein · the same entry in another collection · chain G against G, TM-score 1.00
- Q8R6L9 · AlphaFold monomer V2.0 prediction for small-conductance mechanosensitive channel (Q8R6L9) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P0C0S1 · AlphaFold monomer V2.0 prediction for small-conductance mechanosensitive channel (P0C0S1) · a predicted model of the same protein · chain A against A, TM-score 0.76
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 Q8R6L9
- Every structure of UniProt P0C0S1
- Elsewhere: RCSB PDB 3UDC · PDBe 3UDC · UniProt Q8R6L9 · UniProt P0C0S1
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