Research workbench
Cryo-EM structure of microtubule-bound KIF7 in the ADP state
Analyse Cryo-EM structure of microtubule-bound KIF7 in the ADP state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MLQ
- Type
- protein
- Length
- 1,164 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1A chain; Tubulin beta chain; Kinesin-like protein KIF7
- UniProt
- P02550, P02554, Q2M1P5
- Ligands
- GTP, GDP, TA1, ADP, MG
- Pockets
- 17 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1A chain | protein | 411 | 41% helix, 13% strand | P02550 |
| B | Tubulin beta chain | protein | 426 | 39% helix, 17% strand | P02554 |
| C | Kinesin-like protein KIF7 | protein | 327 | 30% helix, 22% strand | Q2M1P5 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- TA1 · Taxol · ligand · chains B
- ADP · Adenosine-5'-diphosphate · ligand · chains C
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.85 | 0.86 | 107 | empty |
| 2 | 324 | 0.84 | 0.94 | 49 | MG, GTP |
| 3 | 133 | 0.78 | 0.95 | 36 | empty |
| 4 | 113 | 0.76 | 0.95 | 27 | empty |
| 5 | 58 | 0.69 | 0.96 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1950 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 855 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 278 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6MLQ · Cryo-EM structure of microtubule-bound Kif7 in the ADP state · the same entry in another collection · chain A against A, TM-score 1.00
- P02550 · AlphaFold monomer V2.0 prediction for tubulin alpha-1A chain (P02550) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q2M1P5 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF7 (Q2M1P5) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 P02550
- Every structure of UniProt P02554
- Every structure of UniProt Q2M1P5
- Elsewhere: RCSB PDB 6MLQ · PDBe 6MLQ · UniProt P02550 · UniProt P02554 · UniProt Q2M1P5
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