Research workbench
Tubulin darpin cryo structure
Analyse Tubulin darpin cryo structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NQU
- Type
- protein
- Length
- 1,004 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, MG
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 428 | 46% helix, 17% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 421 | 50% 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
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 394 | 0.75 | 0.86 | 50 | GTP, MG |
| 2 | 483 | 0.68 | 0.79 | 46 | empty |
| 3 | 356 | 0.60 | 0.77 | 40 | empty |
| 4 | 203 | 0.60 | 0.81 | 34 | GDP |
| 5 | 77 | 0.59 | 0.88 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1402 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 919 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5NQU · Tubulin Darpin cryo structure · 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 5NQU · PDBe 5NQU · UniProt P81947 · UniProt Q6B856
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.