Research workbench
Rhcc cocrystallized with capb
Analyse Rhcc cocrystallized with capb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YBK
- Type
- protein
- Length
- 205 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetrabrachion
- UniProt
- Q54436
- Ligands
- BEQ, SO4
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 95% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Tetrabrachion | protein | 52 | 94% helix, 0% strand | Q54436 |
| C | Tetrabrachion | protein | 49 | 96% helix, 0% strand | Q54436 |
Ligands and binding sites
- BEQ · N-(carboxymethyl)-N,N-dimethyl-3-[(1-oxododecyl)amino]-1-propanaminium inner salt · ligand · chains C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.83 | 0.99 | 16 | empty |
| 2 | 121 | 0.81 | 0.98 | 20 | empty |
| 3 | 91 | 0.77 | 0.98 | 18 | empty |
| 4 | 57 | 0.55 | 0.89 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1112 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1104 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1098 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1096 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 69 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1YBK · RHCC cocrystallized with CAPB · 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 Q54436
- Elsewhere: RCSB PDB 1YBK · PDBe 1YBK · UniProt Q54436
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