MolNFT v1 · #163626 · protein
S. pombe microtubule decorated with CUT7 motor domain in the amppnp state
6S8M · Kinesin-like protein CUT7: “S. pombe microtubule decorated with CUT7 motor domain in the amppnp state”. Electron microscopy, 5 ligands (ANP, GDP, EPB), 19 pockets (best druggability 0.84). MolNFT v1 #163626 on GenesisL1: 3D…
- PDB
- 6S8M
- Type
- protein
- Length
- 1,202 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-like protein CUT7; Tubulin beta chain; Tubulin alpha-1 chain
- UniProt
- P24339, P05219, P04688
- Ligands
- ANP, GDP, EPB, GTP, MG
- Pockets
- 19 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Kinesin-like protein CUT7 | protein | 344 | 25% helix, 15% strand | P24339 |
| B | Tubulin beta chain | protein | 429 | 41% helix, 16% strand | P05219 |
| A | Tubulin alpha-1 chain | protein | 429 | 40% helix, 13% strand | P04688 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains K
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- EPB · 7,11-dihydroxy-8,8,10,12,16-pentamethyl-3-[1-methyl-2-(2-methyl-thiazol-4-yl)vinyl]-4,17-dioxabicyclo[14.1.0]heptadecane-5,9-dione · ligand · chains B
- GTP · Guanosine-5'-triphosphate · ligand · chains B, A
- MG · Magnesium ion · metal · chains 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.84 | 0.94 | 43 | GTP |
| 2 | 1039 | 0.80 | 0.82 | 93 | empty |
| 3 | 76 | 0.76 | 0.98 | 24 | empty |
| 4 | 217 | 0.64 | 0.83 | 38 | GDP |
| 5 | 69 | 0.63 | 0.91 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–A · 2150 Ų buried · 24 hydrogen bonds · protein-protein
- K–A · 991 Ų buried · 13 hydrogen bonds · protein-protein
- K–B · 898 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6S8M · S. pombe microtubule decorated with Cut7 motor domain in the AMPPNP state · the same entry in another collection · chain K against K, TM-score 1.00
- P04688 · AlphaFold monomer V2.0 prediction for tubulin alpha-1 chain (P04688) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P05219 · AlphaFold monomer V2.0 prediction for tubulin beta chain (P05219) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P24339 · AlphaFold monomer V2.0 prediction for kinesin-like protein CUT7 (P24339) · a predicted model of the same protein · chain K against A, TM-score 0.89
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 P24339
- Every structure of UniProt P05219
- Every structure of UniProt P04688
- Elsewhere: RCSB PDB 6S8M · PDBe 6S8M · UniProt P24339 · UniProt P05219 · UniProt P04688
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