MolNFT v1 · #139591 · protein
Crystal structure of T2R-ttl-demecolcine complex
5XKE · Tubulin alpha-1B chain: “Crystal structure of T2R-ttl-demecolcine complex”. X-ray diffraction, 5 ligands (GTP, LON, GDP), 20 pockets (best druggability 0.87). MolNFT v1 #139591 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5XKE
- Type
- protein
- Length
- 2,181 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain; Stathmin-4; Uncharacterized protein
- UniProt
- Q2XVP4, F2Z5B2, P63043, E1BQ43
- Ligands
- GTP, LON, GDP, MG, CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 43% helix, 19% strand | Q2XVP4 |
| B | Tubulin beta chain | protein | 428 | 48% helix, 19% strand | F2Z5B2 |
| C | Tubulin alpha-1B chain | protein | 440 | 45% helix, 16% strand | Q2XVP4 |
| D | Tubulin beta chain | protein | 421 | 48% helix, 19% strand | F2Z5B2 |
| E | Stathmin-4 | protein | 121 | 76% helix, 13% strand | P63043 |
| F | Uncharacterized protein | protein | 334 | 31% helix, 21% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- LON · (7S)-1,2,3,10-tetramethoxy-7-(methylamino)-6,7-dihydro-5H-benzo[a]heptalen-9-one · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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 | 626 | 0.87 | 0.92 | 75 | GTP, MG, LON |
| 2 | 775 | 0.85 | 0.88 | 97 | GTP, MG, LON |
| 3 | 1171 | 0.83 | 0.84 | 119 | GDP, MG |
| 4 | 214 | 0.75 | 0.90 | 41 | empty |
| 5 | 890 | 0.72 | 0.77 | 63 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1651 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1492 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1411 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 953 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 852 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5XKE · Crystal structure of T2R-TTL-Demecolcine 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 F2Z5B2
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 5XKE · PDBe 5XKE · UniProt Q2XVP4 · UniProt F2Z5B2 · UniProt P63043 · UniProt E1BQ43
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