Research workbench
30MER structure of lumazine synthase from salmonella typhimurium LT2
Analyse 30MER structure of lumazine synthase from salmonella typhimurium LT2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NQ4
- Type
- protein
- Length
- 4,620 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6,7-dimethyl-8-ribityllumazine synthase
- EC
- 2.5.1.78
- UniProt
- P66038
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 23% 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, U, V, W, X, Y, Z, 1, 2, 3, 4 | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 154 | 47% helix, 23% strand | P66038 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 40 copies · chains A, E, B, C, D, F, G, H, I, J, K, O, L, M, N, P, T, Q, R, S, U, Y, V, W, X, Z, 1, 2, 3, 4
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.87 | 0.88 | 95 | SO4 |
| 2 | 1044 | 0.87 | 0.88 | 96 | SO4 |
| 3 | 1096 | 0.87 | 0.88 | 96 | SO4 |
| 4 | 1027 | 0.86 | 0.87 | 92 | SO4 |
| 5 | 1001 | 0.86 | 0.87 | 93 | SO4 |
Interfaces
57 interfaces between chains.
- 1–2 · 1378 Ų buried · 14 hydrogen bonds · protein-protein
- M–N · 1372 Ų buried · 14 hydrogen bonds · protein-protein
- P–Q · 1371 Ų buried · 13 hydrogen bonds · protein-protein
- P–T · 1367 Ų buried · 14 hydrogen bonds · protein-protein
- X–Y · 1367 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3NQ4 · 30mer structure of Lumazine synthase from Salmonella typhimurium LT2 · 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 P66038
- Elsewhere: RCSB PDB 3NQ4 · PDBe 3NQ4 · UniProt P66038
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