Research workbench
Crystal structures of a pentameric fungal and an icosahedral plant lumazine synthase reveals the structural basis for differences in assembly
Analyse Crystal structures of a pentameric fungal and an icosahedral plant lumazine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C41
- Type
- protein
- Length
- 1,650 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lumazine synthase
- EC
- 2.5.1.78
- UniProt
- Q9UVT8
- Ligands
- LMZ, SO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Lumazine synthase (EC 2.5.1.78) | protein | 165 | 50% helix, 18% strand | Q9UVT8 |
Ligands and binding sites
- LMZ · 5-nitroso-6-ribityl-amino-2,4(1H,3H)-pyrimidinedione · ligand · 10 copies · chains A, E, B, C, D, F, J, G, H, I
- SO4 · Sulfate ion · ion · 20 copies · chains A, E, B, C, D, F, J, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.81 | 0.82 | 55 | SO4 |
| 2 | 982 | 0.81 | 0.82 | 55 | SO4 |
| 3 | 318 | 0.75 | 0.86 | 38 | SO4, LMZ |
| 4 | 323 | 0.74 | 0.86 | 40 | SO4, LMZ |
| 5 | 295 | 0.74 | 0.87 | 35 | SO4, LMZ |
Interfaces
10 interfaces between chains.
- B–C · 1642 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1639 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 1630 Ų buried · 27 hydrogen bonds · protein-protein
- A–E · 1630 Ų buried · 24 hydrogen bonds · protein-protein
- F–J · 1628 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1C41 · Crystal structures of a pentameric fungal and an icosahedral plant lumazine synthase… · the same entry in another collection · chain J against J, TM-score 1.00
- Q9UVT8 · AlphaFold monomer V2.0 prediction for 6,7-dimethyl-8-ribityllumazine synthase (Q9UVT8) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9UVT8
- Elsewhere: RCSB PDB 1C41 · PDBe 1C41 · UniProt Q9UVT8
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