MolNFT v1 · #110074 · protein
Crystal structure of encm (crystallized with 4 mm NADPH)
4XLO · FAD-dependent oxygenase encm: “Crystal structure of encm (crystallized with 4 mm NADPH)”. X-ray diffraction, 1 ligand (FAD), 12 pockets (best druggability 0.89). MolNFT v1 #110074 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4XLO
- Type
- protein
- Length
- 1,841 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD-dependent oxygenase encm
- UniProt
- Q9KHK2
- Ligands
- FAD
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FAD-dependent oxygenase encm | protein | 458 | 35% helix, 24% strand | Q9KHK2 |
| B, C, D | FAD-dependent oxygenase encm | protein | 461 | 35% helix, 24% strand | Q9KHK2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.89 | 0.94 | 89 | FAD |
| 2 | 780 | 0.89 | 0.92 | 99 | FAD |
| 3 | 896 | 0.88 | 0.90 | 108 | FAD |
| 4 | 723 | 0.88 | 0.92 | 97 | FAD |
| 5 | 362 | 0.79 | 0.89 | 45 | empty |
Interfaces
4 interfaces between chains.
- B–D · 2256 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 2181 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 485 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 88 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (flavinylation).
Compared structures
- 4XLO · Crystal Structure of EncM (crystallized with 4 mM NADPH) · 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 4XLO · PDBe 4XLO · UniProt Q9KHK2
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