MolNFT v1 · #75866 · protein
The crystal structure of ycei-like family protein from pseudomonas syringae
3Q34: “The crystal structure of ycei-like family protein from pseudomonas syringae”. X-ray diffraction, 1 ligand (UQ8), 9 pockets (best druggability 0.88). MolNFT v1 #75866 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3Q34
- Type
- protein
- Length
- 688 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ycei-like family protein
- UniProt
- Q48EL2
- Ligands
- UQ8
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ycei-like family protein | protein | 174 | 21% helix, 51% strand | Q48EL2 |
| B | Ycei-like family protein | protein | 170 | 21% helix, 52% strand | Q48EL2 |
| C | Ycei-like family protein | protein | 171 | 21% helix, 53% strand | Q48EL2 |
| D | Ycei-like family protein | protein | 173 | 18% helix, 51% strand | Q48EL2 |
Ligands and binding sites
- UQ8 · Ubiquinone-8 · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.88 | 0.94 | 74 | UQ8 |
| 2 | 490 | 0.88 | 0.94 | 72 | UQ8 |
| 3 | 524 | 0.87 | 0.92 | 71 | UQ8 |
| 4 | 526 | 0.86 | 0.92 | 68 | UQ8 |
| 5 | 667 | 0.84 | 0.89 | 68 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1390 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1363 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 536 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 529 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 63 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3Q34 · The crystal structure of YceI-like family protein from Pseudomonas syringae · 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 Q48EL2
- Elsewhere: RCSB PDB 3Q34 · PDBe 3Q34 · UniProt Q48EL2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.