Research workbench
Plasmodium falciparum kinesin-5 motor domain bound to amppnp, complexed with 14 protofilament microtubule.
Analyse Plasmodium falciparum kinesin-5 motor domain bound to amppnp, complexed with 14… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NBA
- Type
- protein
- Length
- 1,185 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain; Kinesin motor domain-containing…
- UniProt
- Q2XVP4, P02554, W7K044
- Ligands
- GTP, G2P, ANP, MG
- Pockets
- 14 · best druggability 0.84
Structure
electron microscopy · 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 | 48% helix, 18% strand | P02554 |
| K | Kinesin motor domain-containing PROTEIN,KINESIN motor domain-containing protein | protein | 331 | 35% helix, 29% strand | W7K044 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- G2P · Phosphomethylphosphonic acid guanylate ester · ligand · chains B
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains K
- MG · Magnesium ion · metal · 3 copies · chains A, B, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.84 | 0.85 | 91 | empty |
| 2 | 732 | 0.83 | 0.87 | 108 | GTP, MG |
| 3 | 302 | 0.73 | 0.86 | 32 | empty |
| 4 | 57 | 0.70 | 0.97 | 17 | empty |
| 5 | 387 | 0.70 | 0.82 | 46 | ANP, MG |
Interfaces
3 interfaces between chains.
- A–B · 1759 Ų buried · 22 hydrogen bonds · protein-protein
- A–K · 827 Ų buried · 6 hydrogen bonds · protein-protein
- B–K · 664 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7NBA · Plasmodium falciparum kinesin-5 motor domain bound to AMPPNP, complexed with 14… · 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 P02554
- Every structure of UniProt W7K044
- Elsewhere: RCSB PDB 7NBA · PDBe 7NBA · UniProt Q2XVP4 · UniProt P02554 · UniProt W7K044
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