Research workbench
CAKIP3[2-482] - AMP-pnp in complex with a microtubule
Analyse CAKIP3[2-482] - 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
- 7TQX
- Type
- protein
- Length
- 1,229 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Kinesin-like protein
- UniProt
- Q2XVP4, A0A287AGU7, A0A1D8PKA4
- Ligands
- GTP, GDP, TA1, ANP, MG
- Pockets
- 16 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 440 | 45% helix, 16% strand | Q2XVP4 |
| B | Tubulin beta-2B chain | protein | 429 | 48% helix, 18% strand | A0A287AGU7 |
| K | Kinesin-like protein | protein | 360 | 32% helix, 21% strand | A0A1D8PKA4 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- TA1 · Taxol · ligand · chains B
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains K
- MG · Magnesium ion · metal · 2 copies · chains A, B, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.84 | 0.96 | 43 | GTP, MG |
| 2 | 1173 | 0.83 | 0.84 | 129 | empty |
| 3 | 244 | 0.64 | 0.82 | 37 | GDP |
| 4 | 332 | 0.59 | 0.77 | 30 | TA1 |
| 5 | 287 | 0.58 | 0.77 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2011 Ų buried · 21 hydrogen bonds · protein-protein
- A–K · 1322 Ų buried · 14 hydrogen bonds · protein-protein
- B–K · 628 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7TQX · CaKip3[2-482] - AMP-PNP in complex with a microtubule · the same entry in another collection · chain A against A, 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 Q2XVP4
- Every structure of UniProt A0A287AGU7
- Every structure of UniProt A0A1D8PKA4
- Elsewhere: RCSB PDB 7TQX · PDBe 7TQX · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt A0A1D8PKA4
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