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Crystal structure of lumazine synthase from brucella abortus (orthorhombic form at 3.05 ångströms)
Analyse Crystal structure of lumazine synthase from brucella abortus (orthorhombic form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XN1
- Type
- protein
- Length
- 1,474 residues
- Chains
- 10
- 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
- P61711
- Ligands
- NA, PO4, SO4
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 56% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, G, I | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 148 | 57% helix, 20% strand | P61711 |
| B | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 147 | 56% helix, 21% strand | P61711 |
| C, D | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 147 | 56% helix, 22% strand | P61711 |
| E | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 148 | 54% helix, 21% strand | P61711 |
| H | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 146 | 55% helix, 21% strand | P61711 |
| J | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 147 | 55% helix, 22% strand | P61711 |
Ligands and binding sites
- NA · Sodium ion · metal · 7 copies · chains A, E, B, D, F, J, G, H
- PO4 · Phosphate ion · ion · 24 copies · chains A, E, B, C, D, F, J, G, H, I
- SO4 · Sulfate ion · ion · 15 copies · chains B, C, D, E, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.82 | 0.88 | 45 | NA, PO4 |
| 2 | 535 | 0.81 | 0.87 | 46 | PO4 |
| 3 | 525 | 0.80 | 0.87 | 44 | PO4, NA |
| 4 | 519 | 0.80 | 0.86 | 43 | NA, PO4 |
| 5 | 517 | 0.80 | 0.86 | 43 | PO4 |
Interfaces
20 interfaces between chains.
- H–I · 1396 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 1386 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1383 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 1382 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1374 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1XN1 · Crystal Structure Of Lumazine Synthase From Brucella Abortus (Orthorhombic Form At 3.05… · the same entry in another collection · chain J against J, TM-score 1.00
- P61711 · AlphaFold monomer V2.0 prediction for 6,7-dimethyl-8-ribityllumazine synthase 2 (P61711) · a predicted model of the same protein · chain B 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 P61711
- Elsewhere: RCSB PDB 1XN1 · PDBe 1XN1 · UniProt P61711
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