Research workbench
CAKIP3[2-482] - ADP-alfx in complex with a microtubule
Analyse CAKIP3[2-482] - ADP-alfx in complex with a microtubule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TQY
- Type
- protein
- Length
- 1,235 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-like protein; Tubulin alpha-1B chain; Tubulin beta-2B chain
- UniProt
- A0A1D8PKA4, Q2XVP4, A0A287AGU7
- Ligands
- AF3, ADP, GTP, GDP, TA1, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Kinesin-like protein | protein | 365 | 35% helix, 26% strand | A0A1D8PKA4 |
| A | Tubulin alpha-1B chain | protein | 441 | 42% helix, 16% strand | Q2XVP4 |
| B | Tubulin beta-2B chain | protein | 429 | 48% helix, 19% strand | A0A287AGU7 |
Ligands and binding sites
- AF3 · Aluminum fluoride · ligand · chains K
- ADP · Adenosine-5'-diphosphate · ligand · chains K
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- TA1 · Taxol · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains K, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.83 | 0.95 | 43 | GTP, MG |
| 2 | 1051 | 0.81 | 0.82 | 84 | empty |
| 3 | 273 | 0.62 | 0.80 | 40 | GDP |
| 4 | 241 | 0.61 | 0.80 | 32 | empty |
| 5 | 377 | 0.60 | 0.77 | 51 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1996 Ų buried · 24 hydrogen bonds · protein-protein
- K–A · 1030 Ų buried · 8 hydrogen bonds · protein-protein
- K–B · 811 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7TQY · CaKip3[2-482] - ADP-AlFx in complex with a microtubule · the same entry in another collection · chain K against K, 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 A0A1D8PKA4
- Every structure of UniProt Q2XVP4
- Every structure of UniProt A0A287AGU7
- Elsewhere: RCSB PDB 7TQY · PDBe 7TQY · UniProt A0A1D8PKA4 · UniProt Q2XVP4 · UniProt A0A287AGU7
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