MolNFT v1 · #176444 · protein
Gmpcpp microtubule complex
7DMZ · Tubulin alpha-1B chain: “Gmpcpp microtubule complex”. Electron microscopy, 4 ligands (GTP, TAJ, G2P), 20 pockets (best druggability 0.85). MolNFT v1 #176444 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7DMZ
- Type
- protein
- Length
- 2,562 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain
- UniProt
- Q2XVP4, P02554
- Ligands
- GTP, TAJ, G2P, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B | Tubulin alpha-1B chain | protein | 428 | 42% helix, 16% strand | Q2XVP4 |
| E, C, F | Tubulin beta chain | protein | 426 | 42% helix, 17% strand | P02554 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains D, C, A, B, E
- TAJ · taccalonolide AJ · ligand · 3 copies · chains E, C, F
- G2P · Phosphomethylphosphonic acid guanylate ester · ligand · 3 copies · chains A, E, C, D, F
- MG · Magnesium ion · metal · 2 copies · chains A, B
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 | 412 | 0.85 | 0.93 | 54 | GTP, MG |
| 2 | 430 | 0.84 | 0.92 | 53 | G2P |
| 3 | 565 | 0.84 | 0.89 | 75 | G2P |
| 4 | 371 | 0.83 | 0.92 | 52 | GTP |
| 5 | 57 | 0.73 | 0.98 | 22 | empty |
Interfaces
7 interfaces between chains.
- D–C · 1922 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 1876 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1746 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 1684 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 393 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7DMZ · GMPCPP microtubule complex · the same entry in another collection · chain D against D, 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 Q2XVP4
- Every structure of UniProt P02554
- Elsewhere: RCSB PDB 7DMZ · PDBe 7DMZ · UniProt Q2XVP4 · UniProt P02554
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