MolNFT v1 · #140762 · protein
Crystal structure of T2R-ttl-Y28 complex
5YL2 · Tubulin alpha-1B chain: “Crystal structure of T2R-ttl-Y28 complex”. X-ray diffraction, 6 ligands (GTP, 8WU, GDP), 20 pockets (best druggability 0.88). MolNFT v1 #140762 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YL2
- 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; Tubulin tyrosine ligase
- UniProt
- Q2XVP4, A0A287AGU7, P63043, E1BQ43
- Ligands
- GTP, 8WU, GDP, ACP, MG, CA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 46% helix, 18% strand | Q2XVP4 |
| B | Tubulin beta chain | protein | 428 | 49% helix, 19% strand | A0A287AGU7 |
| C | Tubulin alpha-1B chain | protein | 440 | 46% helix, 18% strand | Q2XVP4 |
| D | Tubulin beta chain | protein | 421 | 49% helix, 20% strand | A0A287AGU7 |
| E | Stathmin-4 | protein | 121 | 76% helix, 13% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 334 | 33% helix, 21% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, C, D
- 8WU · (E)-1-(5-methoxy-2,2-dimethyl-chromen-8-yl)-3-(4-methoxy-3-oxidanyl-phenyl)prop-2-en-1-one · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 573 | 0.88 | 0.94 | 86 | GTP, MG, 8WU |
| 2 | 780 | 0.84 | 0.87 | 100 | GTP, MG, 8WU |
| 3 | 919 | 0.84 | 0.85 | 118 | GDP, MG |
| 4 | 146 | 0.78 | 0.95 | 28 | empty |
| 5 | 845 | 0.72 | 0.77 | 62 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1614 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1445 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1437 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 910 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 833 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5YL2 · Crystal structure of T2R-TTL-Y28 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 A0A287AGU7
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 5YL2 · PDBe 5YL2 · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63043 · UniProt E1BQ43
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