Research workbench
Z-SBTUB3 photoswitch bound to tubulin-darpin D1 complex
Analyse Z-SBTUB3 photoswitch bound to tubulin-darpin D1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZWB
- Type
- protein
- Length
- 1,023 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Designed ankyrin repeat protein (darpin) D1
- UniProt
- P81947, Q6B856
- Ligands
- GTP, GDP, QRN, MG
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 45% helix, 17% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 431 | 49% helix, 19% strand | Q6B856 |
| F | Designed ankyrin repeat protein (darpin) D1 | protein | 155 | 53% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- QRN · 5-[2-(1,3-benzothiazol-2-yl)ethyl]-2-methoxy-phenol · ligand · chains A, B
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.83 | 0.84 | 114 | GTP, MG, QRN |
| 2 | 196 | 0.62 | 0.83 | 38 | GDP |
| 3 | 150 | 0.54 | 0.81 | 29 | empty |
| 4 | 178 | 0.54 | 0.80 | 24 | empty |
| 5 | 51 | 0.53 | 0.89 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1341 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 918 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6ZWB · Z-SBTub3 photoswitch bound to tubulin-DARPin D1 complex · 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 P81947
- Every structure of UniProt Q6B856
- Elsewhere: RCSB PDB 6ZWB · PDBe 6ZWB · UniProt P81947 · UniProt Q6B856
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