Research workbench

Yeast PRP3 C-terminal fragment 296-469

Analyse Yeast PRP3 C-terminal fragment 296-469 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YHU
Type: protein
Length: 382 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U4/U6 small nuclear ribonucleoprotein PRP3
UniProt: Q03338
Ligands: YT3
Pockets: 4 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	U4/U6 small nuclear ribonucleoprotein PRP3	protein	133	31% helix, 32% strand	Q03338
B	U4/U6 small nuclear ribonucleoprotein PRP3	protein	132	31% helix, 35% strand	Q03338
C	U4/U6 small nuclear ribonucleoprotein PRP3	protein	117	33% helix, 32% strand	Q03338

Ligands and binding sites

YT3 · Yttrium (III) ion · metal · 4 copies · chains A, B, C

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

Pockets

4 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	68	0.61	0.90	22	empty
2	235	0.49	0.75	34	empty
3	172	0.44	0.75	31	empty
4	56	0.33	0.77	14	empty

Interfaces

2 interfaces between chains.

A–B · 774 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 762 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

4YHU · Yeast Prp3 C-terminal fragment 296-469 · the same entry in another collection · chain A against A, TM-score 1.00
Q03338 · AlphaFold monomer V2.0 prediction for U4/U6 small nuclear ribonucleoprotein PRP3 (Q03338) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q03338
Elsewhere: RCSB PDB 4YHU · PDBe 4YHU · UniProt Q03338

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