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Crystal structure of ribosomal oxygenase NO66 dimer mutant

Analyse Crystal structure of ribosomal oxygenase NO66 dimer mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Y4R
Type: protein
Length: 889 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bifunctional lysine-specific demethylase and histidyl- hydroxylase NO66
EC: 1.14.11.-, 1.14.11.27
UniProt: Q9H6W3
Ligands: NI
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bifunctional lysine-specific demethylase and histidyl- hydroxylase NO66 (EC 1.14.11.-, 1.14.11.27)	protein	447	36% helix, 20% strand	Q9H6W3
B	Bifunctional lysine-specific demethylase and histidyl- hydroxylase NO66 (EC 1.14.11.-, 1.14.11.27)	protein	442	36% helix, 18% strand	Q9H6W3

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · chains A, B
ACT · Acetate ion · additive · chains A

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	334	0.71	0.84	54	empty
2	444	0.70	0.81	60	NI
3	303	0.70	0.84	46	empty
4	402	0.69	0.81	73	NI, ACT
5	148	0.57	0.82	23	empty

Interfaces

1 interface between chains.

A–B · 3393 Å² buried · 51 hydrogen bonds · protein-protein

Compared structures

4Y4R · Crystal structure of ribosomal oxygenase NO66 dimer mutant · the same entry in another collection · chain A against A, TM-score 1.00
Q9H6W3 · AlphaFold monomer V2.0 prediction for ribosomal oxygenase 1 (Q9H6W3) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9H6W3
Elsewhere: RCSB PDB 4Y4R · PDBe 4Y4R · UniProt Q9H6W3

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