MolNFT v1 · #140778 · protein
Crystal structure of T2R-ttl-millepachine complex
5YLJ · Tubulin alpha-1B chain: “Crystal structure of T2R-ttl-millepachine complex”. X-ray diffraction, 6 ligands (GTP, 8X0, GDP), 20 pockets (best druggability 0.86). MolNFT v1 #140778 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5YLJ
- 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, 8X0, GDP, ACP, MG, CA
- Pockets
- 20 · best druggability 0.86
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 | 44% helix, 18% strand | Q2XVP4 |
| B | Tubulin beta chain | protein | 428 | 49% helix, 19% strand | A0A287AGU7 |
| C | Tubulin alpha-1B chain | protein | 440 | 45% helix, 17% strand | Q2XVP4 |
| D | Tubulin beta chain | protein | 421 | 48% helix, 20% strand | A0A287AGU7 |
| E | Stathmin-4 | protein | 121 | 77% helix, 13% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 334 | 33% helix, 22% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- 8X0 · (E)-1-(5-methoxy-2,2-dimethyl-chromen-8-yl)-3-(4-methoxyphenyl)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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.86 | 0.88 | 119 | GTP, MG, 8X0 |
| 2 | 1192 | 0.82 | 0.83 | 122 | GDP, MG |
| 3 | 199 | 0.80 | 0.94 | 36 | GTP, MG |
| 4 | 571 | 0.80 | 0.85 | 70 | 8X0 |
| 5 | 153 | 0.77 | 0.94 | 28 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1620 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1481 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1469 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 921 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 856 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5YLJ · Crystal structure of T2R-TTL-Millepachine 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 5YLJ · PDBe 5YLJ · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63043 · UniProt E1BQ43
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