Research workbench
Human kinesin-5 motor domain in the amppnp state bound to microtubules
Analyse Human kinesin-5 motor domain in the amppnp state bound to microtubules in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TA4
- Type
- protein
- Length
- 1,217 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin beta chain; Tubulin alpha-1B chain; Kinesin-like protein KIF11
- UniProt
- P02554, Q2XVP4, P52732
- Ligands
- G2P, GTP, ANP, MG
- Pockets
- 13 · best druggability 0.89
Structure
electron microscopy · 3 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Tubulin beta chain | protein | 429 | 50% helix, 10% strand | P02554 |
| A | Tubulin alpha-1B chain | protein | 438 | 49% helix, 7% strand | Q2XVP4 |
| K | Kinesin-like protein KIF11 | protein | 350 | 33% helix, 22% strand | P52732 |
Ligands and binding sites
- G2P · Phosphomethylphosphonic acid guanylate ester · ligand · chains B
- GTP · Guanosine-5'-triphosphate · ligand · chains B, A
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains K
- MG · Magnesium ion · metal · 3 copies · chains B, A, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.89 | 0.91 | 163 | G2P, GTP, MG |
| 2 | 388 | 0.86 | 0.94 | 55 | empty |
| 3 | 882 | 0.84 | 0.86 | 96 | empty |
| 4 | 81 | 0.74 | 0.96 | 26 | empty |
| 5 | 56 | 0.73 | 0.99 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1531 Ų buried · 21 hydrogen bonds · protein-protein
- B–K · 831 Ų buried · 24 hydrogen bonds · protein-protein
- A–K · 633 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6TA4 · Human kinesin-5 motor domain in the AMPPNP state bound to microtubules · the same entry in another collection · chain B against B, 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 P02554
- Every structure of UniProt Q2XVP4
- Every structure of UniProt P52732
- Elsewhere: RCSB PDB 6TA4 · PDBe 6TA4 · UniProt P02554 · UniProt Q2XVP4 · UniProt P52732
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