Research workbench
Crystal structure of T2R-ttl bound with po-7
Analyse Crystal structure of T2R-ttl bound with po-7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XI7
- 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, PO7, GDP, ACP, MG, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 437 | 44% helix, 18% strand | A0A0R4I993 |
| B | Tubulin beta chain | protein | 424 | 47% helix, 20% strand | A0A0R4I995 |
| C | Tubulin alpha chain | protein | 440 | 46% helix, 18% strand | A0A0R4I993 |
| D | Tubulin beta chain | protein | 421 | 48% helix, 19% strand | A0A0R4I995 |
| E | Stathmin-4 | protein | 120 | 77% helix, 14% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 309 | 28% helix, 24% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- PO7 · (6Z)-3-[[2,5-bis(fluoranyl)phenyl]methylidene]-6-[(4-tert-butyl-1H-imidazol-5-yl)methylidene]piperazine-2, 5-dione · 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 · 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 | 935 | 0.86 | 0.88 | 110 | GTP, MG, PO7 |
| 2 | 887 | 0.84 | 0.86 | 105 | GTP, MG, PO7 |
| 3 | 1184 | 0.82 | 0.83 | 109 | GDP, MG |
| 4 | 190 | 0.81 | 0.96 | 43 | empty |
| 5 | 843 | 0.71 | 0.77 | 60 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1588 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1518 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1484 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 915 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 853 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5XI7 · Crystal structure of T2R-TTL bound with PO-7 · 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 5XI7 · PDBe 5XI7 · UniProt A0A0R4I993 · UniProt A0A0R4I995 · UniProt P63043 · UniProt E1BQ43
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