MolNFT v1 · #31924 · protein

Crystal structure of the PRP19 U-box dimer

2BAY · Pre-mRNA splicing factor PRP19: “Crystal structure of the PRP19 U-box dimer”. X-ray diffraction, 6 pockets (best druggability 0.71). MolNFT v1 #31924 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2BAY
Type: protein
Length: 340 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pre-mRNA splicing factor PRP19
UniProt: P32523
Pockets: 6 · best druggability 0.71

Structure

x-ray diffraction · 5 distinct chains · 25% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pre-mRNA splicing factor PRP19	protein	56	25% helix, 21% strand	P32523
C	Pre-mRNA splicing factor PRP19	protein	55	25% helix, 18% strand	P32523
D	Pre-mRNA splicing factor PRP19	protein	56	25% helix, 21% strand	P32523
E	Pre-mRNA splicing factor PRP19	protein	59	24% helix, 19% strand	P32523
F	Pre-mRNA splicing factor PRP19	protein	58	24% helix, 22% strand	P32523

Pockets

6 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	1170	0.71	0.75	67	empty
2	64	0.49	0.84	13	empty
3	111	0.48	0.80	28	empty
4	92	0.43	0.79	27	empty
5	67	0.37	0.78	12	empty

Interfaces

10 interfaces between chains.

E–F · 968 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 639 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 555 Å² buried · 3 hydrogen bonds · protein-protein
C–F · 167 Å² buried · 0 hydrogen bonds · protein-protein
D–E · 154 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2BAY · Crystal structure of the Prp19 U-box dimer · the same entry in another collection · chain E against E, TM-score 1.00
P32523 · AlphaFold monomer V2.0 prediction for pre-mRNA-processing factor 19 (P32523) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 P32523
Elsewhere: RCSB PDB 2BAY · PDBe 2BAY · UniProt P32523

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