Research workbench
Crystal structure of T2R-ttl-8WR complex
Analyse Crystal structure of T2R-ttl-8WR complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YL4
- Type
- protein
- Length
- 2,151 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain; Stathmin-4; Tubulin tyrosine ligase
- UniProt
- A0A0R4I993, A0A0R4I995, P63043, E1BQ43
- Ligands
- GTP, GDP, 8WR, ACP, MG, CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 437 | 45% helix, 18% strand | A0A0R4I993 |
| B | Tubulin beta chain | protein | 424 | 49% helix, 20% strand | A0A0R4I995 |
| C | Tubulin alpha chain | protein | 440 | 46% helix, 17% strand | A0A0R4I993 |
| D | Tubulin beta chain | protein | 421 | 48% helix, 19% strand | A0A0R4I995 |
| E | Stathmin-4 | protein | 120 | 77% helix, 13% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 309 | 28% helix, 23% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- 8WR · (3Z,6Z)-3-[(4-tert-butyl-1H-imidazol-5-yl)methylidene]-6-[[3-(phenylcarbonyl)phenyl]methylidene]piperazine-2, 5-dione · ligand · chains A, B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.87 | 0.89 | 100 | GTP, MG, 8WR |
| 2 | 915 | 0.84 | 0.85 | 112 | GDP, MG |
| 3 | 386 | 0.78 | 0.88 | 56 | GTP, MG |
| 4 | 141 | 0.76 | 0.94 | 33 | empty |
| 5 | 650 | 0.73 | 0.79 | 70 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1599 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1504 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1434 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 924 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 868 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5YL4 · Crystal structure of T2R-ttl-8WR 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 A0A0R4I993
- Every structure of UniProt A0A0R4I995
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 5YL4 · PDBe 5YL4 · UniProt A0A0R4I993 · UniProt A0A0R4I995 · UniProt P63043 · UniProt E1BQ43
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