Research workbench
Tubulin dimers from a 13-protofilament, taxol stabilized microtubule
Analyse Tubulin dimers from a 13-protofilament, taxol stabilized microtubule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WVR
- Type
- protein
- Length
- 1,712 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain
- UniProt
- P81947, E1BJB1
- Ligands
- GTP, GDP, TA1, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tubulin alpha-1B chain | protein | 430 | 45% helix, 19% strand | P81947 |
| B, D | Tubulin beta chain | protein | 426 | 48% helix, 20% strand | E1BJB1 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, A, D
- TA1 · Taxol · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.82 | 0.96 | 42 | GTP, MG |
| 2 | 188 | 0.81 | 0.96 | 44 | GTP, MG |
| 3 | 647 | 0.80 | 0.85 | 83 | GDP |
| 4 | 227 | 0.62 | 0.82 | 36 | GDP |
| 5 | 300 | 0.59 | 0.77 | 32 | TA1 |
Interfaces
3 interfaces between chains.
- A–B · 1979 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1978 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 1471 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6WVR · Tubulin dimers from a 13-protofilament, Taxol stabilized 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 P81947
- Every structure of UniProt E1BJB1
- Elsewhere: RCSB PDB 6WVR · PDBe 6WVR · UniProt P81947 · UniProt E1BJB1
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