Research workbench
Cryo-EM structure of microtubule-bound KLP61F motor domain in the amppnp state
Analyse Cryo-EM structure of microtubule-bound KLP61F motor domain in the amppnp state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VPO
- Type
- protein
- Length
- 1,173 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 KLP61F
- UniProt
- P02550, P02554, P46863
- Ligands
- GTP, GDP, ANP, MG
- Pockets
- 18 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1A chain | protein | 422 | 43% helix, 16% strand | P02550 |
| B | Tubulin beta chain | protein | 421 | 48% helix, 19% strand | P02554 |
| C | Kinesin-like protein KLP61F | protein | 330 | 33% helix, 25% strand | P46863 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains C
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.83 | 0.95 | 43 | GTP, MG |
| 2 | 1152 | 0.80 | 0.81 | 83 | empty |
| 3 | 82 | 0.72 | 0.96 | 20 | empty |
| 4 | 69 | 0.71 | 0.96 | 24 | empty |
| 5 | 58 | 0.68 | 0.95 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1905 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 906 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 845 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6VPO · Cryo-EM structure of microtubule-bound KLP61F motor domain in the AMPPNP 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 0.97
- P46863 · AlphaFold monomer V2.0 prediction for kinesin-like protein KLP61F (P46863) · a predicted model of the same protein · chain C against A, TM-score 0.92
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 P46863
- Elsewhere: RCSB PDB 6VPO · PDBe 6VPO · UniProt P02550 · UniProt P02554 · UniProt P46863
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