Research workbench
Hela-tubulin in complex with cryptophycin 52
Analyse Hela-tubulin in complex with cryptophycin 52 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LXB
- Type
- protein
- Length
- 6,928 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-3 chain
- UniProt
- P68363, Q13509
- Ligands
- GTP, YGY, GDP
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O | Tubulin alpha-1B chain | protein | 436 | 41% helix, 11% strand | P68363 |
| B, D, F, H, J, L, N, P | Tubulin beta-3 chain | protein | 430 | 44% helix, 13% strand | Q13509 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 8 copies · chains A, C, E, G, I, K, M, O
- YGY · Cryptophycin 52 · ligand · 8 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
- GDP · Guanosine-5'-diphosphate · ligand · 8 copies · chains B, D, F, H, J, L, N, P
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 | 972 | 0.83 | 0.85 | 95 | GTP |
| 2 | 1032 | 0.83 | 0.84 | 105 | GTP |
| 3 | 988 | 0.83 | 0.84 | 99 | GTP |
| 4 | 1015 | 0.83 | 0.84 | 105 | GTP |
| 5 | 999 | 0.83 | 0.84 | 89 | GTP |
Interfaces
16 interfaces between chains.
- C–F · 1020 Ų buried · 5 hydrogen bonds · protein-protein
- M–P · 1019 Ų buried · 5 hydrogen bonds · protein-protein
- G–J · 1016 Ų buried · 5 hydrogen bonds · protein-protein
- B–O · 1015 Ų buried · 5 hydrogen bonds · protein-protein
- I–L · 1015 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7LXB · HeLa-tubulin in complex with cryptophycin 52 · the same entry in another collection · chain P against P, 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 P68363
- Every structure of UniProt Q13509
- Elsewhere: RCSB PDB 7LXB · PDBe 7LXB · UniProt P68363 · UniProt Q13509
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