MolNFT v1 · #119086 · protein
Enzyme-substrate complex of ni-quercetinase
5FLI · Quercetinase qued: “Enzyme-substrate complex of ni-quercetinase”. X-ray diffraction, 2 ligands (QUE, NI), 20 pockets (best druggability 0.84). MolNFT v1 #119086 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FLI
- 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
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Quercetinase qued (EC 1.13.11.24) | protein | 183 | 10% helix, 38% strand | A2VA43 |
Ligands and binding sites
- QUE · 3,5,7,3',4'-pentahydroxyflavone · ligand · 11 copies · chains A, B, C, D, E, F, G, H, J, K, L
- NI · Nickel (II) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, 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 | 727 | 0.84 | 0.88 | 111 | empty |
| 2 | 1107 | 0.81 | 0.83 | 123 | empty |
| 3 | 534 | 0.81 | 0.87 | 89 | empty |
| 4 | 124 | 0.79 | 0.96 | 28 | QUE |
| 5 | 116 | 0.79 | 0.97 | 29 | QUE |
Interfaces
21 interfaces between chains.
- E–F · 1980 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1971 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 1968 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1946 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1945 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5FLI · enzyme-substrate complex of Ni-quercetinase · the same entry in another collection · chain A against A, 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 5FLI · PDBe 5FLI · UniProt A2VA43
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