MolNFT v1 · #181654 · protein
Hela-tubulin in complex with cryptophycin 1
7M18 · Tubulin beta-3 chain: “Hela-tubulin in complex with cryptophycin 1”. Electron microscopy, 3 ligands (YNP, GDP, GTP), 20 pockets (best druggability 0.84). MolNFT v1 #181654 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7M18
- Type
- protein
- Length
- 6,904 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin beta-3 chain; Tubulin alpha-1B chain
- UniProt
- Q13509, P68363
- Ligands
- YNP, GDP, GTP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 40% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, F, H, J, L, N, P | Tubulin beta-3 chain | protein | 427 | 40% helix, 13% strand | Q13509 |
| A, C, E, G, I, K, M, O | Tubulin alpha-1B chain | protein | 436 | 41% helix, 8% strand | P68363 |
Ligands and binding sites
- YNP · Cryptophycin 1 · ligand · 8 copies · chains B, A, D, C, F, E, H, G, J, I, L, K, N, M, P, O
- GDP · Guanosine-5'-diphosphate · ligand · 8 copies · chains B, D, F, H, J, L, N, P
- GTP · Guanosine-5'-triphosphate · ligand · 8 copies · chains A, C, E, G, I, K, M, O
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 | 1178 | 0.84 | 0.85 | 122 | GTP |
| 2 | 880 | 0.84 | 0.86 | 99 | GTP |
| 3 | 1140 | 0.84 | 0.85 | 118 | GTP |
| 4 | 1120 | 0.81 | 0.83 | 94 | GTP |
| 5 | 1144 | 0.81 | 0.83 | 97 | GTP |
Interfaces
16 interfaces between chains.
- B–O · 976 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 973 Ų buried · 6 hydrogen bonds · protein-protein
- M–P · 973 Ų buried · 5 hydrogen bonds · protein-protein
- I–L · 972 Ų buried · 5 hydrogen bonds · protein-protein
- K–N · 970 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7M18 · HeLa-tubulin in complex with cryptophycin 1 · the same entry in another collection · chain O against O, 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 Q13509
- Every structure of UniProt P68363
- Elsewhere: RCSB PDB 7M18 · PDBe 7M18 · UniProt Q13509 · UniProt P68363
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