Research workbench
TUBULIN:STATHMIN-like domain complex
Analyse TUBULIN:STATHMIN-like domain complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F6R
- Type
- protein
- Length
- 1,091 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain; Stathmin-like domain R1; Designed ankyrin repeat…
- UniProt
- D0VWZ0, D0VWY9
- Ligands
- GTP, GDP, MG, SO4
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 437 | 46% helix, 18% strand | D0VWZ0 |
| B | Tubulin beta chain | protein | 431 | 48% helix, 18% strand | D0VWY9 |
| C | Stathmin-like domain R1 | protein | 64 | 63% helix, 17% strand | — |
| D | Designed ankyrin repeat protein (darpin) D2 | protein | 159 | 56% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.80 | 0.82 | 92 | GTP, MG |
| 2 | 237 | 0.69 | 0.85 | 32 | MES |
| 3 | 453 | 0.67 | 0.78 | 35 | empty |
| 4 | 443 | 0.64 | 0.77 | 49 | empty |
| 5 | 265 | 0.60 | 0.79 | 40 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1509 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1473 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 783 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 680 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4F6R · Tubulin:Stathmin-like domain 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 D0VWZ0
- Every structure of UniProt D0VWY9
- Elsewhere: RCSB PDB 4F6R · PDBe 4F6R · UniProt D0VWZ0 · UniProt D0VWY9
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