Research workbench
Structural basis of backwards motion in kinesin-14: minus-end directed NKN664 in the amppnp state
Analyse Structural basis of backwards motion in kinesin-14: minus-end directed NKN664… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HNW
- Type
- protein
- Length
- 1,167 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Protein claret SEGREGATIONAL,KINESIN heavy…
- UniProt
- P81947, Q6B856, P20480
- Ligands
- GTP, GDP, TA1, ANP, MG
- Pockets
- 19 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 412 | 44% helix, 14% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 426 | 44% helix, 14% strand | Q6B856 |
| K | Protein claret SEGREGATIONAL,KINESIN heavy chain isoform 5C | protein | 329 | 29% helix, 23% strand | P20480 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- TA1 · Taxol · ligand · chains B
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains K
- MG · Magnesium ion · metal · 2 copies · chains A, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.83 | 0.96 | 42 | MG, GTP |
| 2 | 1000 | 0.82 | 0.83 | 83 | empty |
| 3 | 213 | 0.81 | 0.94 | 52 | empty |
| 4 | 211 | 0.62 | 0.82 | 33 | MG, ANP |
| 5 | 212 | 0.57 | 0.80 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1927 Ų buried · 36 hydrogen bonds · protein-protein
- A–K · 636 Ų buried · 7 hydrogen bonds · protein-protein
- B–K · 570 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5HNW · Structural basis of backwards motion in kinesin-14: minus-end directed nKn664 in the… · the same entry in another collection · chain A against A, TM-score 1.00
- P20480 · AlphaFold monomer V2.0 prediction for protein claret segregational (P20480) · a predicted model of the same protein · chain K against A, TM-score 0.83
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 P81947
- Every structure of UniProt Q6B856
- Every structure of UniProt P20480
- Elsewhere: RCSB PDB 5HNW · PDBe 5HNW · UniProt P81947 · UniProt Q6B856 · UniProt P20480
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