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Crystal structure of NOP9 in complex with ITS1 RNA

Analyse Crystal structure of NOP9 in complex with ITS1 RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WPI
Type: protein + RNA
Length: 614 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleolar protein 9; RNA (47-mer)
UniProt: P47077
Ligands: TCE
Pockets: 5 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleolar protein 9	protein	548	72% helix, 0% strand	P47077
B	RNA (47-mer)	rna	39	—	—
C	RNA (47-mer)	rna	27	—	—

Ligands and binding sites

TCE · 3,3',3''-phosphanetriyltripropanoic acid · ligand · chains A
GOL · Glycerol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	436	0.59	0.76	26	empty
2	191	0.46	0.75	21	empty
3	67	0.34	0.77	16	empty
4	67	0.27	0.73	14	empty
5	55	0.24	0.72	14	empty

Interfaces

2 interfaces between chains.

A–B · 739 Å² buried · 19 hydrogen bonds · protein-nucleic
B–C · 346 Å² buried · 18 hydrogen bonds · nucleic-nucleic

Compared structures

6WPI · Crystal structure of Nop9 in complex with ITS1 RNA · the same entry in another collection · chain A against A, TM-score 1.00
P47077 · AlphaFold monomer V2.0 prediction for nucleolar protein 9 (P47077) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P47077
Elsewhere: RCSB PDB 6WPI · PDBe 6WPI · UniProt P47077

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