MolNFT v1 · #134246 · protein
Near-atomic resolution cryo-EM reconstruction of doubly bound taxol- and peloruside-stabilized microtubule
5SYE · Tubulin alpha chain: “Near-atomic resolution cryo-EM reconstruction of doubly bound taxol- and peloruside-stabilized microtubule”. Electron microscopy, 5 ligands (GTP, GDP, TA1), 11 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 5SYE
- Type
- protein
- Length
- 853 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain
- UniProt
- B6A7R0, P02554
- Ligands
- GTP, GDP, TA1, POU, MG
- Pockets
- 11 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 427 | 42% helix, 15% strand | B6A7R0 |
| B | Tubulin beta chain | protein | 426 | 48% helix, 18% strand | P02554 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- TA1 · Taxol · ligand · chains B
- POU · Peloruside A · ligand · chains B
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.83 | 0.94 | 52 | GTP, MG |
| 2 | 83 | 0.72 | 0.95 | 25 | empty |
| 3 | 323 | 0.57 | 0.76 | 36 | TA1 |
| 4 | 240 | 0.56 | 0.78 | 32 | empty |
| 5 | 183 | 0.54 | 0.79 | 35 | GDP |
Interfaces
1 interface between chains.
- A–B · 1972 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5SYE · Near-atomic resolution cryo-EM reconstruction of doubly bound Taxol- and… · the same entry in another collection · chain A against A, TM-score 1.00
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 B6A7R0
- Every structure of UniProt P02554
- Elsewhere: RCSB PDB 5SYE · PDBe 5SYE · UniProt B6A7R0 · UniProt P02554
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