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Structure of an oxygenase

Analyse Structure of an oxygenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3K2O
Type: protein
Length: 671 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
EC: 1.14.11.-
UniProt: Q6NYC1
Ligands: NI, NA, CL, PO4
Pockets: 6 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 (EC 1.14.11.-)	protein	335	43% helix, 21% strand	Q6NYC1
B	Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 (EC 1.14.11.-)	protein	336	42% helix, 21% strand	Q6NYC1

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · 6 copies · chains A, B
PO4 · Phosphate ion · ion · 3 copies · chains A, B
ACT · Acetate ion · additive · 2 copies · chains A, B
GOL · Glycerol · additive · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1134	0.85	0.86	97	GOL
2	518	0.70	0.80	52	CL, ACT
3	500	0.70	0.80	53	NI, ACT
4	92	0.35	0.74	15	empty
5	85	0.33	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 1093 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

3K2O · Structure of an oxygenase · the same entry in another collection · chain A against A, TM-score 1.00
Q6NYC1 · AlphaFold monomer V2.0 prediction for bifunctional arginine demethylase and… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q6NYC1
Elsewhere: RCSB PDB 3K2O · PDBe 3K2O · UniProt Q6NYC1

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