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Crystal structure of lumazine synthase from brucella abortus bound to 5-nitro-6-(D-ribitylamino)-2,4(1H,3H) pyrimidinedione
Analyse Crystal structure of lumazine synthase from brucella abortus bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T13
- Type
- protein
- Length
- 740 residues
- Chains
- 5
- 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
- Q44668
- Ligands
- INI, PO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 150 | 53% helix, 21% strand | Q44668 |
| B, C | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 147 | 55% helix, 20% strand | Q44668 |
| D, E | 6,7-dimethyl-8-ribityllumazine synthase (EC 2.5.1.78) | protein | 148 | 55% helix, 21% strand | Q44668 |
Ligands and binding sites
- INI · 5-nitro-6-ribityl-amino-2,4(1H,3H)-pyrimidinedione · ligand · 5 copies · chains A, E, B, C, D
- PO4 · Phosphate ion · ion · 5 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.80 | 0.91 | 38 | PO4, INI |
| 2 | 340 | 0.80 | 0.90 | 37 | PO4, INI |
| 3 | 339 | 0.80 | 0.89 | 35 | PO4, INI |
| 4 | 333 | 0.79 | 0.89 | 35 | PO4, INI |
| 5 | 328 | 0.79 | 0.89 | 38 | PO4, INI |
Interfaces
5 interfaces between chains.
- A–B · 1452 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1343 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1325 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1322 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1322 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1T13 · Crystal Structure Of Lumazine Synthase From Brucella Abortus Bound To… · the same entry in another collection · chain B against B, 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 Q44668
- Elsewhere: RCSB PDB 1T13 · PDBe 1T13 · UniProt Q44668
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