MolNFT v1 · #172240 · protein
Z-SBTUB2 photoswitch bound to tubulin-darpin D1 complex
6ZWC · Tubulin alpha-1B chain: “Z-SBTUB2 photoswitch bound to tubulin-darpin D1 complex”. X-ray diffraction, 4 ligands (GTP, GDP, QRQ), 10 pockets (best druggability 0.84). MolNFT v1 #172240 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6ZWC
- Type
- protein
- Length
- 1,022 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, QRQ, MG
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 436 | 45% helix, 17% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 431 | 47% helix, 18% strand | Q6B856 |
| F | Designed ankyrin repeat protein (darpin) D1 | protein | 155 | 54% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- QRQ · 2-[2-(3,4,5-trimethoxyphenyl)ethyl]-1,3-benzothiazole · 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
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.84 | 0.85 | 110 | GTP, MG, QRQ |
| 2 | 198 | 0.62 | 0.83 | 32 | GDP |
| 3 | 156 | 0.53 | 0.80 | 28 | empty |
| 4 | 180 | 0.52 | 0.79 | 23 | empty |
| 5 | 104 | 0.46 | 0.79 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1308 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 967 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6ZWC · Z-SBTub2 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 6ZWC · PDBe 6ZWC · UniProt P81947 · UniProt Q6B856
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