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
- 1C2Y
- Type
- protein
- Length
- 3,100 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (lumazine synthase)
- EC
- 2.5.1.78
- UniProt
- Q9XH32
- Ligands
- LMZ
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T | Protein (lumazine synthase) (EC 2.5.1.78) | protein | 155 | 49% helix, 21% strand | Q9XH32 |
Ligands and binding sites
- LMZ · 5-nitroso-6-ribityl-amino-2,4(1H,3H)-pyrimidinedione · ligand · 20 copies · chains A, E, B, C, D, F, J, G, H, I, K, O, L, M, N, P, T, Q, R, S
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 | 998 | 0.86 | 0.87 | 91 | LMZ |
| 2 | 1079 | 0.86 | 0.87 | 101 | LMZ |
| 3 | 1003 | 0.86 | 0.87 | 89 | LMZ |
| 4 | 957 | 0.86 | 0.87 | 91 | LMZ |
| 5 | 967 | 0.86 | 0.87 | 93 | LMZ |
Interfaces
35 interfaces between chains.
- H–I · 1320 Ų buried · 28 hydrogen bonds · protein-protein
- F–J · 1319 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 1310 Ų buried · 27 hydrogen bonds · protein-protein
- L–M · 1310 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1309 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1C2Y · Crystal structures of a pentameric fungal and an icosahedral plant lumazine synthase… · the same entry in another collection · chain T against T, 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 Q9XH32
- Elsewhere: RCSB PDB 1C2Y · PDBe 1C2Y · UniProt Q9XH32
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