Research workbench
Crystal structure of T2R-ttl-MPC6827 complex
Analyse Crystal structure of T2R-ttl-MPC6827 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XKF
- Type
- protein
- Length
- 2,180 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, 88U, GDP, MG, CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 46% helix, 19% strand | Q2XVP4 |
| B | Tubulin beta chain | protein | 427 | 48% helix, 20% strand | A0A287AGU7 |
| C | Tubulin alpha-1B chain | protein | 440 | 46% helix, 17% strand | Q2XVP4 |
| D | Tubulin beta chain | protein | 421 | 48% helix, 19% 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, B, C, D
- 88U · N-(4-methoxyphenyl)-N,2-dimethyl-quinazolin-4-amine · 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.81 | 0.94 | 36 | GTP, MG |
| 2 | 816 | 0.81 | 0.84 | 80 | GDP, MG |
| 3 | 161 | 0.80 | 0.96 | 31 | 88U |
| 4 | 463 | 0.79 | 0.86 | 68 | 88U |
| 5 | 157 | 0.77 | 0.94 | 36 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1596 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1536 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1477 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 907 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 859 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5XKF · Crystal structure of T2R-TTL-MPC6827 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 5XKF · PDBe 5XKF · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63043 · UniProt E1BQ43
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