Research workbench
CAKIP3[2-436]-L2-MUTANT(HSKHC) - AMP-pnp in complex with a microtubule
Analyse CAKIP3[2-436]-L2-MUTANT(HSKHC) - AMP-pnp 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
- 7TR1
- Type
- protein
- Length
- 1,216 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-like PROTEIN,KINESIN-1 heavy chain; Tubulin alpha-1B chain; Tubulin beta-2B chain
- UniProt
- C4YNU9, Q2XVP4, A0A287AGU7
- Ligands
- ANP, GTP, GDP, TA1, MG
- Pockets
- 15 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Kinesin-like PROTEIN,KINESIN-1 heavy chain | protein | 346 | 34% helix, 23% strand | C4YNU9 |
| A | Tubulin alpha-1B chain | protein | 441 | 44% helix, 15% strand | Q2XVP4 |
| B | Tubulin beta-2B chain | protein | 429 | 46% helix, 19% strand | A0A287AGU7 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · 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, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.84 | 0.95 | 40 | GTP, MG |
| 2 | 1083 | 0.80 | 0.82 | 76 | empty |
| 3 | 475 | 0.66 | 0.79 | 66 | MG, ANP |
| 4 | 291 | 0.63 | 0.80 | 39 | empty |
| 5 | 277 | 0.61 | 0.79 | 36 | GDP |
Interfaces
3 interfaces between chains.
- A–B · 1956 Ų buried · 17 hydrogen bonds · protein-protein
- K–A · 818 Ų buried · 8 hydrogen bonds · protein-protein
- K–B · 788 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7TR1 · CaKip3[2-436]-L2-mutant(HsKHC) - AMP-PNP in complex with a microtubule · the same entry in another collection · chain K against K, TM-score 1.00
- Q2XVP4 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (Q2XVP4) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 C4YNU9
- Every structure of UniProt Q2XVP4
- Every structure of UniProt A0A287AGU7
- Elsewhere: RCSB PDB 7TR1 · PDBe 7TR1 · UniProt C4YNU9 · UniProt Q2XVP4 · UniProt A0A287AGU7
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