Research workbench
Undecorated GDP microtubule
Analyse Undecorated GDP microtubule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DPV
- Type
- protein
- Length
- 5,124 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain
- UniProt
- Q2XVP4, P02554
- Ligands
- GTP, GDP, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, J, K, L | Tubulin alpha-1B chain | protein | 428 | 48% helix, 18% strand | Q2XVP4 |
| B, D, F, G, H, I | Tubulin beta chain | protein | 426 | 50% helix, 19% strand | P02554 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, H, C, I, E, G, F, J, B, K, D, L
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F, G, H, I
- MG · Magnesium ion · metal · 6 copies · chains A, H, C, I, E, G, F, J, B, K, D, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.84 | 0.96 | 48 | GTP, MG |
| 2 | 254 | 0.84 | 0.96 | 46 | GTP, MG |
| 3 | 261 | 0.83 | 0.95 | 46 | GTP, MG |
| 4 | 259 | 0.83 | 0.95 | 46 | GTP, MG |
| 5 | 256 | 0.83 | 0.95 | 47 | GTP, MG |
Interfaces
17 interfaces between chains.
- F–J · 1836 Ų buried · 17 hydrogen bonds · protein-protein
- D–L · 1835 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 1835 Ų buried · 17 hydrogen bonds · protein-protein
- C–I · 1831 Ų buried · 17 hydrogen bonds · protein-protein
- B–K · 1831 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6DPV · Undecorated GDP microtubule · 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 Q2XVP4
- Every structure of UniProt P02554
- Elsewhere: RCSB PDB 6DPV · PDBe 6DPV · UniProt Q2XVP4 · UniProt P02554
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