MolNFT v1 · #66235 · protein
Tubulin-TN16 : RB3 stathmin-like domain complex
3HKD · Tubulin alpha chain: “Tubulin-TN16 : RB3 stathmin-like domain complex”. X-ray diffraction, 4 ligands (GTP, GDP, N16), 19 pockets (best druggability 0.83). MolNFT v1 #66235 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3HKD
- 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
- P63043
- Ligands
- GTP, GDP, N16, MG
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 428 | 43% helix, 15% strand | — |
| B | Tubulin beta chain | protein | 420 | 44% helix, 14% strand | — |
| C | Tubulin alpha chain | protein | 429 | 42% helix, 14% strand | — |
| D | Tubulin beta chain | protein | 427 | 43% helix, 12% strand | — |
| E | Stathmin-4 | protein | 123 | 41% helix, 9% 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
- N16 · (3Z,5S)-5-benzyl-3-[1-(phenylamino)ethylidene]pyrrolidine-2,4-dione · 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.83 | 0.84 | 98 | GTP, MG, N16 |
| 2 | 913 | 0.83 | 0.84 | 94 | GTP, MG, N16 |
| 3 | 1117 | 0.82 | 0.83 | 124 | GDP, MG |
| 4 | 670 | 0.73 | 0.79 | 66 | empty |
| 5 | 572 | 0.69 | 0.78 | 42 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1541 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1324 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1297 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 986 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 741 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 P63043
- Elsewhere: RCSB PDB 3HKD · PDBe 3HKD · UniProt P63043
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.