MolNFT v1 · #142818 · protein
The structure of ch-II-77-tubulin complex
6AGK · Tubulin alpha-1B chain: “The structure of ch-II-77-tubulin complex”. X-ray diffraction, 6 ligands (GTP, 9WR, GDP), 20 pockets (best druggability 0.86). MolNFT v1 #142818 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6AGK
- Type
- protein
- Length
- 2,151 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Tubulin tyrosine ligase
- UniProt
- Q2XVP4, Q6B856, P63043, E1BQ43
- Ligands
- GTP, 9WR, GDP, ACP, MG, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 44% helix, 18% strand | Q2XVP4 |
| B | Tubulin beta-2B chain | protein | 424 | 48% helix, 20% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 47% helix, 16% strand | Q2XVP4 |
| D | Tubulin beta-2B chain | protein | 421 | 48% helix, 19% strand | Q6B856 |
| E | Stathmin-4 | protein | 120 | 76% helix, 13% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 309 | 27% helix, 24% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- 9WR · [6-(3-hydroxy-4-methylphenyl)pyridin-2-yl](3,4,5-trimethoxyphenyl)methanone · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.86 | 0.93 | 65 | GTP, MG, 9WR |
| 2 | 399 | 0.86 | 0.94 | 65 | GTP, MG, 9WR |
| 3 | 608 | 0.81 | 0.86 | 90 | GDP |
| 4 | 961 | 0.77 | 0.80 | 93 | empty |
| 5 | 149 | 0.77 | 0.95 | 32 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1597 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1439 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1366 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 926 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 846 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6AGK · The structure of CH-II-77-tubulin complex · 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 Q2XVP4
- Every structure of UniProt Q6B856
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 6AGK · PDBe 6AGK · UniProt Q2XVP4 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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