MolNFT v1 · #134248 · protein
Cryo-EM reconstruction of zampanolide-bound microtubule
5SYG · Tubulin alpha chain: “Cryo-EM reconstruction of zampanolide-bound microtubule”. Electron microscopy, 4 ligands (GTP, GDP, ZPN), 9 pockets (best druggability 0.80). MolNFT v1 #134248 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5SYG
- Type
- protein
- Length
- 852 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, ZPN, MG
- Pockets
- 9 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 426 | 46% helix, 16% 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
- ZPN · (2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide · 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.80 | 0.94 | 45 | GTP, MG |
| 2 | 322 | 0.64 | 0.80 | 38 | ZPN |
| 3 | 168 | 0.53 | 0.79 | 31 | GDP |
| 4 | 152 | 0.47 | 0.77 | 25 | empty |
| 5 | 147 | 0.44 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1906 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
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 5SYG · PDBe 5SYG · UniProt B6A7R0 · UniProt P02554
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