MolNFT v1 · #66236 · protein
Tubulin-T138067: RB3 stathmin-like domain complex
3HKE · Tubulin alpha chain: “Tubulin-T138067: RB3 stathmin-like domain complex”. X-ray diffraction, 4 ligands (T13, GTP, GDP), 20 pockets (best druggability 0.82). MolNFT v1 #66236 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3HKE
- Type
- protein
- Length
- 1,826 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
- T13, GTP, GDP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 427 | 43% helix, 15% strand | — |
| B | Tubulin beta chain | protein | 420 | 44% helix, 15% strand | — |
| C | Tubulin alpha chain | protein | 428 | 44% helix, 14% strand | — |
| D | Tubulin beta chain | protein | 427 | 43% helix, 15% strand | — |
| E | Stathmin-4 | protein | 124 | 48% helix, 5% strand | P63043 |
Ligands and binding sites
- T13 · 2,3,4,5,6-pentafluoro-N-(3-fluoro-4-methoxyphenyl)benzenesulfonamide · ligand · 4 copies · chains A, B, D, C
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, 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
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.82 | 0.84 | 101 | GTP, MG, T13 |
| 2 | 1067 | 0.82 | 0.83 | 124 | GDP, MG |
| 3 | 1050 | 0.82 | 0.83 | 97 | GTP, MG, T13 |
| 4 | 563 | 0.72 | 0.80 | 63 | empty |
| 5 | 723 | 0.72 | 0.78 | 64 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1553 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1307 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1277 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1006 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 722 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3HKE · Tubulin-T138067: RB3 stathmin-like domain complex · the same entry in another collection · chain C against C, 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 P63043
- Elsewhere: RCSB PDB 3HKE · PDBe 3HKE · UniProt P63043
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