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Crystal structure of human fibrillarin in complex with compound 2A

Analyse Crystal structure of human fibrillarin in complex with compound 2A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SED
Type: protein
Length: 227 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RRNA 2'-O-methyltransferase fibrillarin
EC: 2.1.1.-
UniProt: P22087
Ligands: 8VD
Pockets: 1 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RRNA 2'-O-methyltransferase fibrillarin (EC 2.1.1.-)	protein	227	29% helix, 31% strand	P22087

Ligands and binding sites

8VD · N-(piperidin-4-yl)-6-(trifluoromethyl)pyrimidin-4-amine · ligand · chains A
FMT · Formic acid · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	100	0.48	0.81	26	8VD, FMT

Compared structures

7SED · Crystal structure of human Fibrillarin in complex with compound 2a · the same entry in another collection · chain A against A, TM-score 1.00
P22087 · AlphaFold monomer V2.0 prediction for rRNA 2'-O-methyltransferase fibrillarin (P22087) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P22087
Elsewhere: RCSB PDB 7SED · PDBe 7SED · UniProt P22087

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