MolNFT v1 · #127075 · protein
S. pombe microtubule decorated with CUT7 motor domain in the amppnp state
5MLV · Tubulin alpha-1 chain: “S. pombe microtubule decorated with CUT7 motor domain in the amppnp state”. Electron microscopy, 5 ligands (GTP, ANP, GDP), 20 pockets (best druggability 0.84). MolNFT v1 #127075 on GenesisL1: 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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