MolNFT v1 · #46684 · protein
Lumazine synthase RIBH2 from mesorhizobium loti (gene MLL7281, swiss- prot entry Q986N2) complexed with inhibitor 5-nitro-6-(D- ribitylamino)-2,4(1H,3H) pyrimidinedione
2OBX · 6,7-dimethyl-8-ribityllumazine synthase 1: “Lumazine synthase RIBH2 from mesorhizobium loti (gene MLL7281, swiss- prot entry Q986N2) complexed with…”. X-ray diffraction, 2 ligands (INI, PO4), 19 pockets (best druggability 0.80).…
- PDB
- 2OBX
- Type
- protein
- Length
- 1,471 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6,7-dimethyl-8-ribityllumazine synthase 1
- EC
- 2.5.1.78
- UniProt
- Q986N2
- Ligands
- INI, PO4
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6,7-dimethyl-8-ribityllumazine synthase 1 (EC 2.5.1.78) | protein | 150 | 55% helix, 21% strand | Q986N2 |
| B, C, H | 6,7-dimethyl-8-ribityllumazine synthase 1 (EC 2.5.1.78) | protein | 147 | 54% helix, 21% strand | Q986N2 |
| D, E, I, J | 6,7-dimethyl-8-ribityllumazine synthase 1 (EC 2.5.1.78) | protein | 146 | 53% helix, 21% strand | Q986N2 |
| F, G | 6,7-dimethyl-8-ribityllumazine synthase 1 (EC 2.5.1.78) | protein | 148 | 52% helix, 21% strand | Q986N2 |
Ligands and binding sites
- INI · 5-nitro-6-ribityl-amino-2,4(1H,3H)-pyrimidinedione · ligand · 10 copies · chains A, E, B, C, D, F, J, G, H, I
- PO4 · Phosphate ion · ion · 9 copies · chains A, E, B, C, D, F, G, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.80 | 0.87 | 46 | PO4, INI |
| 2 | 497 | 0.80 | 0.87 | 50 | INI |
| 3 | 110 | 0.80 | 0.98 | 17 | empty |
| 4 | 490 | 0.80 | 0.87 | 45 | PO4, INI |
| 5 | 463 | 0.80 | 0.87 | 41 | PO4, INI |
Interfaces
20 interfaces between chains.
- F–G · 1339 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1330 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1314 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1313 Ų buried · 11 hydrogen bonds · protein-protein
- I–J · 1308 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2OBX · Lumazine synthase RibH2 from Mesorhizobium loti (Gene mll7281, Swiss-Prot entry Q986N2)… · the same entry in another collection · chain J against J, TM-score 1.00
- Q986N2 · AlphaFold monomer V2.0 prediction for 6,7-dimethyl-8-ribityllumazine synthase 2 (Q986N2) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q986N2
- Elsewhere: RCSB PDB 2OBX · PDBe 2OBX · UniProt Q986N2
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