Research workbench

Head region of the yeast spliceosomal U4/U6.U5 tri-snrnp

Analyse Head region of the yeast spliceosomal U4/U6.U5 tri-snrnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GAO
Type: protein + RNA
Length: 2,924 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Small nuclear ribonucleoprotein-associated protein B; Small nuclear ribonucleoprotein sm…
EC: 3.6.4.13
UniProt: P40018, Q02260, Q06217, P43321, Q12330, P54999, P40204, P32639, P33334
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 11 distinct chains · 34% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
k	Small nuclear ribonucleoprotein-associated protein B	protein	80	4% helix, 34% strand	P40018
l	Small nuclear ribonucleoprotein sm D1	protein	91	14% helix, 18% strand	Q02260
m	Small nuclear ribonucleoprotein sm D2	protein	94	21% helix, 37% strand	Q06217
n	Small nuclear ribonucleoprotein sm D3	protein	82	10% helix, 38% strand	P43321
p	Small nuclear ribonucleoprotein E	protein	76	14% helix, 30% strand	Q12330
q	Small nuclear ribonucleoprotein F	protein	72	10% helix, 53% strand	P54999
r	Small nuclear ribonucleoprotein G	protein	69	4% helix, 36% strand	P40204
E	SNU66	protein	338	36% helix, 0% strand	—
B	Pre-mRNA-splicing helicase BRR2 (EC 3.6.4.13)	protein	1710	43% helix, 15% strand	P32639
V	Saccharomyces cerevisiae strain UOA_M2 chromosome 5 sequence	rna	57	—	—
A	Pre-mRNA-splicing factor 8	protein	255	24% helix, 25% strand	P33334

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	493	0.84	0.91	78	empty
2	709	0.84	0.88	89	empty
3	418	0.83	0.91	67	empty
4	796	0.82	0.85	74	empty
5	829	0.78	0.81	98	empty

Interfaces

22 interfaces between chains.

B–V · 3037 Å² buried · 63 hydrogen bonds · protein-nucleic
E–B · 2645 Å² buried · 21 hydrogen bonds · protein-protein
B–A · 2174 Å² buried · 14 hydrogen bonds · protein-protein
k–n · 1065 Å² buried · 17 hydrogen bonds · protein-protein
p–q · 947 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5GAO · Head region of the yeast spliceosomal U4/U6.U5 tri-snRNP · the same entry in another collection · chain A against A, TM-score 1.00
P54999 · AlphaFold monomer V2.0 prediction for small nuclear ribonucleoprotein F (P54999) · a predicted model of the same protein · chain q against A, TM-score 0.92

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 P40018
Every structure of UniProt Q02260
Every structure of UniProt Q06217
Every structure of UniProt P43321
Every structure of UniProt Q12330
Every structure of UniProt P54999
Every structure of UniProt P40204
Every structure of UniProt P32639
Every structure of UniProt P33334
Elsewhere: RCSB PDB 5GAO · PDBe 5GAO · UniProt P40018 · UniProt Q02260 · UniProt Q06217 · UniProt P43321 · UniProt Q12330 · UniProt P54999 · UniProt P40204 · UniProt P32639 · UniProt P33334

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