Research workbench
13PF wildtype microtubule from recombinant human tubulin decorated with kinesin
Analyse 13PF wildtype microtubule from recombinant human tubulin decorated with kinesin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SJ8
- Type
- protein
- Length
- 5,184 residues
- Chains
- 12
- 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, GDP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, J, K, L | Tubulin alpha-1B chain | protein | 435 | 45% helix, 14% strand | P68363 |
| F, D, G, H, I, B | Tubulin beta-3 chain | protein | 429 | 48% helix, 17% strand | Q13509 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, H, C, I, E, G, J, F, K, B, L, D
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains E, F, C, D, G, H, I, A, B
- MG · Magnesium ion · metal · 6 copies · chains A, C, E, J, K, 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 | 391 | 0.86 | 0.94 | 59 | GDP |
| 2 | 334 | 0.84 | 0.94 | 54 | GDP |
| 3 | 379 | 0.84 | 0.93 | 56 | GDP |
| 4 | 245 | 0.83 | 0.96 | 42 | GTP, MG |
| 5 | 233 | 0.83 | 0.96 | 40 | GTP, MG |
Interfaces
17 interfaces between chains.
- J–F · 1960 Ų buried · 22 hydrogen bonds · protein-protein
- E–G · 1959 Ų buried · 21 hydrogen bonds · protein-protein
- K–B · 1954 Ų buried · 20 hydrogen bonds · protein-protein
- A–H · 1948 Ų buried · 21 hydrogen bonds · protein-protein
- L–D · 1941 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7SJ8 · 13pf wildtype microtubule from recombinant human tubulin decorated with kinesin · the same entry in another collection · chain B against B, 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 7SJ8 · PDBe 7SJ8 · UniProt P68363 · UniProt Q13509
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