Research workbench
Plasmodium falciparum kinesin-5 motor domain without nucleotide, complexed with 14 protofilament microtubule.
Analyse Plasmodium falciparum kinesin-5 motor domain without nucleotide, complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NB8
- Type
- protein
- Length
- 1,177 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.4
- Source
- Plasmodium falciparum (isolate 3D7); Sus scrofa
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain; Kinesin-5
- UniProt
- Q2XVP4, P02554, O77382
- Ligands
- GTP, G2P, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · resolution 4.4 · 3 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 428 | 46% helix, 19% strand | Q2XVP4 |
| B | Tubulin beta chain | protein | 426 | 47% helix, 19% strand | P02554 |
| K | Kinesin-5 | protein | 323 | 37% helix, 29% strand | O77382 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- G2P · Phosphomethylphosphonic acid guanylate ester · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.82 | 0.83 | 77 | empty |
| 2 | 510 | 0.80 | 0.87 | 73 | GTP |
| 3 | 305 | 0.80 | 0.91 | 56 | empty |
| 4 | 69 | 0.74 | 0.98 | 19 | empty |
| 5 | 68 | 0.74 | 0.98 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1843 Ų buried · 25 hydrogen bonds · protein-protein
- A–K · 922 Ų buried · 12 hydrogen bonds · protein-protein
- B–K · 544 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7NB8 · Plasmodium falciparum kinesin-5 motor domain without nucleotide, complexed with 14… · the same entry in another collection · chain A against A, TM-score 1.00
- P02554 · AlphaFold monomer V2.0 prediction for tubulin beta chain (P02554) · a predicted model of the same protein · chain B 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 Q2XVP4
- Every structure of UniProt P02554
- Every structure of UniProt O77382
- Elsewhere: RCSB PDB 7NB8 · PDBe 7NB8 · UniProt Q2XVP4 · UniProt P02554 · UniProt O77382
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