MolNFT v1 · #172054 · protein
Microtubule complexed with KIF15 motor domain. symmetrised asymmetric unit
6ZPI · Kinesin-like protein KIF15: “Microtubule complexed with KIF15 motor domain. symmetrised asymmetric unit”. Electron microscopy, 5 ligands (ANP, GTP, GDP), 13 pockets (best druggability 0.80). MolNFT v1 #172054 on GenesisL1: 3D…
- PDB
- 6ZPI
- Type
- protein
- Length
- 1,184 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-like protein KIF15; Tubulin alpha-1B chain; Tubulin beta chain
- UniProt
- Q9NS87, Q2XVP4, P02554
- Ligands
- ANP, GTP, GDP, TA1, MG
- Pockets
- 13 · best druggability 0.80
Structure
electron microscopy · 3 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Kinesin-like protein KIF15 | protein | 332 | 35% helix, 29% strand | Q9NS87 |
| A | Tubulin alpha-1B chain | protein | 426 | 42% helix, 16% strand | Q2XVP4 |
| B | Tubulin beta chain | protein | 426 | 47% helix, 19% strand | P02554 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains C
- 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 C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.80 | 0.92 | 51 | GTP, MG |
| 2 | 1169 | 0.79 | 0.81 | 75 | empty |
| 3 | 317 | 0.72 | 0.85 | 47 | empty |
| 4 | 194 | 0.64 | 0.84 | 33 | empty |
| 5 | 370 | 0.62 | 0.78 | 60 | ANP, MG |
Interfaces
3 interfaces between chains.
- A–B · 2009 Ų buried · 40 hydrogen bonds · protein-protein
- C–B · 660 Ų buried · 7 hydrogen bonds · protein-protein
- C–A · 657 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6ZPI · Microtubule complexed with Kif15 motor domain. Symmetrised asymmetric unit · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NS87 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF15 (Q9NS87) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 Q9NS87
- Every structure of UniProt Q2XVP4
- Every structure of UniProt P02554
- Elsewhere: RCSB PDB 6ZPI · PDBe 6ZPI · UniProt Q9NS87 · UniProt Q2XVP4 · UniProt P02554
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