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Crystal structure of an H/ACA box rnp from pyrococcus furiosus

Analyse Crystal structure of an H/ACA box rnp from pyrococcus furiosus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2HVY
Type: protein + RNA
Length: 625 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H/ACA RNA; Probable tRNA pseudouridine synthase B; Small nucleolar rnp similar to GAR1…
EC: 5.4.99.-
UniProt: Q7LWY0, Q8U029, Q8U1R4, Q8U160
Ligands: ATP, ZN
Pockets: 5 · best druggability 0.79

Structure

x-ray diffraction · 5 distinct chains · 30% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	H/ACA RNA	rna	57	—	—
A	Probable tRNA pseudouridine synthase B (EC 5.4.99.-)	protein	320	28% helix, 33% strand	Q7LWY0
B	Small nucleolar rnp similar to GAR1	protein	74	5% helix, 53% strand	Q8U029
C	Ribosome biogenesis protein NOP10	protein	53	23% helix, 15% strand	Q8U1R4
D	50S ribosomal protein L7AE	protein	121	52% helix, 16% strand	Q8U160

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains E, A, B
ZN · Zinc ion · metal · chains C

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

Pockets

5 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	1185	0.79	0.81	87	empty
2	434	0.62	0.76	35	empty
3	548	0.58	0.73	36	empty
4	132	0.43	0.76	19	empty
5	59	0.40	0.81	13	empty

Interfaces

7 interfaces between chains.

A–C · 1479 Å² buried · 26 hydrogen bonds · protein-protein
E–A · 1300 Å² buried · 28 hydrogen bonds · protein-nucleic
A–B · 899 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 707 Å² buried · 9 hydrogen bonds · protein-protein
E–D · 650 Å² buried · 25 hydrogen bonds · protein-nucleic

Compared structures

2HVY · Crystal structure of an H/ACA box RNP from Pyrococcus furiosus · the same entry in another collection · chain D against D, TM-score 1.00
Q8U160 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L7AE (Q8U160) · a predicted model of the same protein · chain D against A, TM-score 0.99
Q7LWY0 · AlphaFold monomer V2.0 prediction for probable tRNA pseudouridine synthase B (Q7LWY0) · a predicted model of the same protein · chain A against A, TM-score 0.96
Q8U1R4 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein NOP10 (Q8U1R4) · a predicted model of the same protein · chain C against A, TM-score 0.94

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 Q7LWY0
Every structure of UniProt Q8U029
Every structure of UniProt Q8U1R4
Every structure of UniProt Q8U160
Elsewhere: RCSB PDB 2HVY · PDBe 2HVY · UniProt Q7LWY0 · UniProt Q8U029 · UniProt Q8U1R4 · UniProt Q8U160

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