Research workbench
A prototype protein nanocage minimized from carboxysomes with gated oxygen permeability
Analyse A prototype protein nanocage minimized from carboxysomes with gated oxygen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WKC
- Type
- protein
- Length
- 460 residues
- Chains
- 5
- Method
- solid-state nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxysome shell vertex protein ccml
- UniProt
- Q8DKB4
- Pockets
- 7 · best druggability 0.73
Structure
solid-state nmr · 1 distinct chain · 8% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Carboxysome shell vertex protein ccml | protein | 92 | 8% helix, 22% strand | Q8DKB4 |
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.73 | 0.78 | 79 | empty |
| 2 | 252 | 0.58 | 0.79 | 45 | empty |
| 3 | 277 | 0.58 | 0.77 | 42 | empty |
| 4 | 261 | 0.57 | 0.77 | 42 | empty |
| 5 | 235 | 0.56 | 0.78 | 43 | empty |
Interfaces
5 interfaces between chains.
- A–C · 611 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 610 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 609 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 608 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 608 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7WKC · A prototype protein nanocage minimized from carboxysomes with gated oxygen permeability · the same entry in another collection · chain D against D, TM-score 1.00
- Q8DKB4 · AlphaFold monomer V2.0 prediction for carboxysome shell vertex protein ccml (Q8DKB4) · a predicted model of the same protein · chain C against A, TM-score 0.61
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 Q8DKB4
- Elsewhere: RCSB PDB 7WKC · PDBe 7WKC · UniProt Q8DKB4
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