Research workbench
Enzyme-substrate-dioxygen complex of ni-quercetinase
Analyse Enzyme-substrate-dioxygen complex of ni-quercetinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FLJ
- Type
- protein
- Length
- 2,196 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Quercetinase qued
- EC
- 1.13.11.24
- UniProt
- A2VA43
- Ligands
- QUE, NI, OXY
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Quercetinase qued (EC 1.13.11.24) | protein | 182 | 9% helix, 40% strand | A2VA43 |
| B, C, D, E, F, G, H, I, J, K | Quercetinase qued (EC 1.13.11.24) | protein | 183 | 9% helix, 39% strand | A2VA43 |
| L | Quercetinase qued (EC 1.13.11.24) | protein | 184 | 9% helix, 40% strand | A2VA43 |
Ligands and binding sites
- QUE · 3,5,7,3',4'-pentahydroxyflavone · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- NI · Nickel (II) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- OXY · Oxygen molecule · ion · 2 copies · chains C, F
- DMS · Dimethyl sulfoxide · additive · 15 copies · chains A, B, C, D, E, F, G, H, K, I, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.86 | 0.87 | 164 | DMS |
| 2 | 124 | 0.79 | 0.96 | 29 | QUE |
| 3 | 119 | 0.79 | 0.97 | 30 | QUE |
| 4 | 126 | 0.79 | 0.96 | 28 | QUE |
| 5 | 125 | 0.79 | 0.96 | 29 | QUE |
Interfaces
22 interfaces between chains.
- E–F · 1977 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1967 Ų buried · 16 hydrogen bonds · protein-protein
- K–L · 1956 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 1955 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1951 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5FLJ · enzyme-substrate-dioxygen complex of Ni-quercetinase · the same entry in another collection · chain I against I, 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 A2VA43
- Elsewhere: RCSB PDB 5FLJ · PDBe 5FLJ · UniProt A2VA43
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