Research workbench
18-mer hela-tubulin rings in complex with cryptophycin 1
Analyse 18-mer hela-tubulin rings in complex with cryptophycin 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M20
- Type
- protein
- Length
- 7,785 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin beta-3 chain; Tubulin alpha-1B chain
- UniProt
- Q13509, P68363
- Ligands
- GDP, YNP, GTP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, F, H, J, L, N, P, R | Tubulin beta-3 chain | protein | 429 | 43% helix, 16% strand | Q13509 |
| A, C, E, G, I, K, M, O, Q | Tubulin alpha-1B chain | protein | 436 | 41% helix, 10% strand | P68363 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 9 copies · chains B, D, F, H, J, L, N, P, R
- YNP · Cryptophycin 1 · ligand · 9 copies · chains B, A, D, C, F, E, H, G, J, I, L, K, N, M, P, O, R, Q
- GTP · Guanosine-5'-triphosphate · ligand · 9 copies · chains A, C, E, G, I, K, M, O, Q
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 | 1012 | 0.84 | 0.85 | 92 | GTP |
| 2 | 1137 | 0.82 | 0.83 | 100 | GTP |
| 3 | 1098 | 0.82 | 0.83 | 93 | GTP |
| 4 | 1096 | 0.82 | 0.83 | 97 | GTP |
| 5 | 1190 | 0.81 | 0.83 | 105 | GTP |
Interfaces
18 interfaces between chains.
- N–O · 901 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 898 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 897 Ų buried · 1 hydrogen bond · protein-protein
- F–G · 897 Ų buried · 1 hydrogen bond · protein-protein
- H–I · 897 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7M20 · 18-mer HeLa-tubulin rings in complex with Cryptophycin 1 · the same entry in another collection · chain Q against Q, 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 7M20 · PDBe 7M20 · UniProt Q13509 · UniProt P68363
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