Research workbench

Prp8 RH domain from C. merolae

Analyse Prp8 RH domain from C. merolae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NQI
Type: protein
Length: 383 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.75
Source: Cyanidioschyzon merolae (strain 10D)
Molecule: Pre-mRNA splicing factor PRP8
UniProt: M1V7K2
Pockets: 2 · best druggability 0.56

Structure

x-ray diffraction · resolution 2.75 · 2 distinct chains · 46% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pre-mRNA splicing factor PRP8	protein	196	46% helix, 20% strand	M1V7K2
B	Pre-mRNA splicing factor PRP8	protein	187	45% helix, 18% strand	M1V7K2

Ligands and binding sites

BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B

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

Pockets

2 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	295	0.56	0.76	22	empty
2	136	0.37	0.73	19	empty

Interfaces

1 interface between chains.

A–B · 562 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (additive adduct).

Compared structures

6NQI · PRP8 rh domain from C. merolae · the same entry in another collection · chain A against A, TM-score 1.00

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 M1V7K2
Elsewhere: RCSB PDB 6NQI · PDBe 6NQI · UniProt M1V7K2

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.