Research workbench
The crystal structure of encm complexed with dioxygen under 5 bar of oxygen pressure.
Analyse The crystal structure of encm complexed with dioxygen under 5 bar of oxygen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FP3
- Type
- protein
- Length
- 1,832 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative FAD-dependent oxygenase encm
- UniProt
- Q9KHK2
- Ligands
- FAD, OXY
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative FAD-dependent oxygenase encm | protein | 458 | 34% helix, 24% strand | Q9KHK2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- OXY · Oxygen molecule · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.88 | 0.92 | 103 | FAD, OXY |
| 2 | 748 | 0.88 | 0.92 | 100 | FAD, OXY |
| 3 | 791 | 0.88 | 0.91 | 102 | FAD, OXY |
| 4 | 737 | 0.87 | 0.91 | 103 | FAD, OXY |
| 5 | 393 | 0.79 | 0.88 | 49 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2189 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2104 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 513 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 93 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6FP3 · The crystal structure of EncM complexed with dioxygen under 5 bar of oxygen pressure. · 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 Q9KHK2
- Elsewhere: RCSB PDB 6FP3 · PDBe 6FP3 · UniProt Q9KHK2
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