Research workbench
Tubulin-nsc 613862: RB3 stathmin-like domain complex
Analyse Tubulin-nsc 613862: RB3 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
- 3N2K
- Type
- protein
- Length
- 1,827 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain; Stathmin-4
- UniProt
- D0VWZ0, D0VWY9, P63043
- Ligands
- GTP, GDP, K2N, MG
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 428 | 42% helix, 14% strand | D0VWZ0 |
| B | Tubulin beta chain | protein | 420 | 42% helix, 15% strand | D0VWY9 |
| C | Tubulin alpha chain | protein | 429 | 40% helix, 15% strand | D0VWZ0 |
| D | Tubulin beta chain | protein | 427 | 41% helix, 13% strand | D0VWY9 |
| E | Stathmin-4 | protein | 123 | 37% helix, 5% strand | P63043 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
- K2N · ethyl [(2S)-5-amino-2-methyl-3-phenyl-1,2-dihydropyrido[3,4-b]pyrazin-7-yl]carbamate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.84 | 0.87 | 84 | GTP, MG, K2N |
| 2 | 890 | 0.83 | 0.85 | 98 | GTP, MG, K2N |
| 3 | 1144 | 0.82 | 0.83 | 126 | GDP, MG |
| 4 | 680 | 0.73 | 0.79 | 56 | empty |
| 5 | 560 | 0.68 | 0.78 | 38 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1522 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1310 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1289 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1012 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 737 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3N2K · TUBULIN-NSC 613862: RB3 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
- Every structure of UniProt P63043
- Elsewhere: RCSB PDB 3N2K · PDBe 3N2K · UniProt D0VWZ0 · UniProt D0VWY9 · UniProt P63043
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