Research workbench
Pseudo-atomic model of microtubule-bound S.POMBE kinesin-5 motor domain in the amppnp state (based on cryo-electron microscopy experiment): the N-terminus adopts multiple conformations.
Analyse Pseudo-atomic model of microtubule-bound S.POMBE kinesin-5 motor domain in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M5N
- Type
- protein
- Length
- 1,207 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1D chain; Tubulin beta-2B chain; Kinesin-like protein CUT7
- UniProt
- Q2HJ86, Q6B856, P24339
- Ligands
- GTP, GDP, TA1, ANP, MG
- Pockets
- 2 · best druggability 0.34
Structure
electron microscopy · 3 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1D chain | protein | 412 | 0% helix, 0% strand | Q2HJ86 |
| B | Tubulin beta-2B chain | protein | 426 | 0% helix, 0% strand | Q6B856 |
| C | Kinesin-like protein CUT7 | protein | 369 | 0% helix, 0% strand | P24339 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- TA1 · Taxol · ligand · chains B
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains C
- MG · Magnesium ion · metal · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.34 | 0.73 | 21 | empty |
| 2 | 50 | 0.27 | 0.72 | 19 | MG |
Interfaces
3 interfaces between chains.
- A–B · 85 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 39 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5M5N · Pseudo-atomic model of microtubule-bound S.pombe kinesin-5 motor domain in the AMPPNP… · the same entry in another collection · chain A against A, TM-score 1.00
- P24339 · AlphaFold monomer V2.0 prediction for kinesin-like protein CUT7 (P24339) · a predicted model of the same protein · chain C against A, TM-score 0.85
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 Q2HJ86
- Every structure of UniProt Q6B856
- Every structure of UniProt P24339
- Elsewhere: RCSB PDB 5M5N · PDBe 5M5N · UniProt Q2HJ86 · UniProt Q6B856 · UniProt P24339
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