Research workbench
Blub bound to reduced flavin (FMNH2) and molecular oxygen. (clear crystal form)
Analyse Blub bound to reduced flavin (FMNH2) and molecular oxygen. (clear crystal form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ISL
- Type
- protein
- Length
- 1,752 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blub
- UniProt
- Q92PC8
- Ligands
- FNR, OXY
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Blub | protein | 219 | 40% helix, 18% strand | Q92PC8 |
Ligands and binding sites
- FNR · 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydro-2H-benzo[g]pteridin-1-id-10(5H)-yl)-5-O-phosphonato-D-ribitol · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- OXY · Oxygen molecule · ion · 8 copies · chains A, B, C, D, E, F, G, H
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 | 172 | 0.83 | 0.98 | 27 | FNR, OXY |
| 2 | 174 | 0.83 | 0.97 | 32 | OXY, FNR |
| 3 | 176 | 0.83 | 0.97 | 32 | OXY, FNR |
| 4 | 192 | 0.83 | 0.96 | 33 | FNR, OXY |
| 5 | 170 | 0.82 | 0.97 | 33 | FNR, OXY |
Interfaces
13 interfaces between chains.
- A–B · 5011 Ų buried · 68 hydrogen bonds · protein-protein
- C–D · 5000 Ų buried · 69 hydrogen bonds · protein-protein
- G–H · 4994 Ų buried · 58 hydrogen bonds · protein-protein
- E–F · 4946 Ų buried · 57 hydrogen bonds · protein-protein
- A–G · 346 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2ISL · BluB bound to reduced flavin (FMNH2) and molecular oxygen. (clear crystal form) · the same entry in another collection · chain H against H, TM-score 1.00
- Q92PC8 · AlphaFold monomer V2.0 prediction for 5,6-dimethylbenzimidazole synthase (Q92PC8) · a predicted model of the same protein · chain C 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 Q92PC8
- Elsewhere: RCSB PDB 2ISL · PDBe 2ISL · UniProt Q92PC8
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