Research workbench
S. pombe microtubule decorated with CUT7 motor domain in the amppnp state
Analyse S. pombe microtubule decorated with CUT7 motor domain in the amppnp state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MLV
- Type
- protein
- Length
- 7,218 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1 chain; Kinesin-like protein CUT7; Tubulin beta chain
- UniProt
- P04688, P24339, P05219
- Ligands
- GTP, ANP, GDP, EPB, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, M, B, H, K, Q | Tubulin alpha-1 chain | protein | 429 | 40% helix, 13% strand | P04688 |
| G, O, A, D, J, P | Kinesin-like protein CUT7 | protein | 344 | 25% helix, 15% strand | P24339 |
| I, N, C, F, L, R | Tubulin beta chain | protein | 430 | 41% helix, 16% strand | P05219 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains E, F, M, N, B, C, I, H, K, L, Q, R
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 6 copies · chains G, O, A, D, J, P
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains E, I, B, N, C, F, Q, L, R
- 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 · 6 copies · chains I, N, C, F, L, R
- MG · Magnesium ion · metal · 6 copies · chains G, O, A, D, J, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.84 | 0.94 | 45 | GTP |
| 2 | 320 | 0.84 | 0.94 | 46 | GTP |
| 3 | 264 | 0.83 | 0.95 | 47 | GDP |
| 4 | 274 | 0.83 | 0.94 | 50 | GDP |
| 5 | 256 | 0.82 | 0.94 | 49 | GDP |
Interfaces
29 interfaces between chains.
- Q–R · 2254 Ų buried · 28 hydrogen bonds · protein-protein
- K–L · 2235 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 2224 Ų buried · 25 hydrogen bonds · protein-protein
- M–N · 2223 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2221 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- P04688 · AlphaFold monomer V2.0 prediction for tubulin alpha-1 chain (P04688) · a predicted model of the same protein · chain E 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 I 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 P 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 P04688
- Every structure of UniProt P24339
- Every structure of UniProt P05219
- Elsewhere: RCSB PDB 5MLV · PDBe 5MLV · UniProt P04688 · UniProt P24339 · UniProt P05219
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