MolNFT v1 · #137575 · protein + RNA

Structure of yeast U6 snrnp with 2'-phosphate terminated U6 RNA

5VSU · U4/U6 snrna-associated-splicing factor PRP24: “Structure of yeast U6 snrnp with 2'-phosphate terminated U6 RNA”. X-ray diffraction, 11 pockets (best druggability 0.79). MolNFT v1 #137575 on GenesisL1: 3D structure, binding sites and…

PDB: 5VSU
Type: protein + RNA
Length: 1,038 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U4/U6 snrna-associated-splicing factor PRP24; U6 snrna-associated sm-like protein LSM2…
UniProt: P49960, P38203, P57743, P40070, P40089, Q06406, P53905, P47093
Pockets: 11 · best druggability 0.79

Structure

x-ray diffraction · 9 distinct chains · 24% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	U4/U6 snrna-associated-splicing factor PRP24	protein	387	39% helix, 28% strand	P49960
B	U6 snrna-associated sm-like protein LSM2	protein	98	31% helix, 36% strand	P38203
C	U6 snrna-associated sm-like protein LSM3	protein	81	11% helix, 60% strand	P57743
D	U6 snrna-associated sm-like protein LSM4	protein	65	15% helix, 49% strand	P40070
E	U6 snrna-associated sm-like protein LSM5	protein	87	7% helix, 48% strand	P40089
F	U6 snrna-associated sm-like protein LSM6	protein	77	13% helix, 51% strand	Q06406
G	U6 snrna-associated sm-like protein LSM7	protein	70	10% helix, 56% strand	P53905
H	U6 snrna-associated sm-like protein LSM8	protein	100	14% helix, 36% strand	P47093
I	Saccharomyces cerevisiae strain T8 chromosome XII sequence	rna	73	—	—

Pockets

11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	889	0.79	0.82	74	empty
2	917	0.75	0.79	82	empty
3	577	0.64	0.76	34	empty
4	235	0.62	0.82	38	empty
5	76	0.51	0.85	19	empty

Interfaces

21 interfaces between chains.

A–I · 2836 Å² buried · 83 hydrogen bonds · protein-nucleic
B–C · 1367 Å² buried · 19 hydrogen bonds · protein-protein
B–H · 1267 Å² buried · 19 hydrogen bonds · protein-protein
E–G · 1074 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 902 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

5VSU · Structure of yeast U6 snRNP with 2'-phosphate terminated U6 RNA · the same entry in another collection · chain F against F, TM-score 1.00
P40070 · AlphaFold monomer V2.0 prediction for U6 snrna-associated sm-like protein LSM4 (P40070) · a predicted model of the same protein · chain D against A, TM-score 0.98
P53905 · AlphaFold monomer V2.0 prediction for U6 snrna-associated sm-like protein LSM7 (P53905) · a predicted model of the same protein · chain G against A, TM-score 0.96
P40089 · AlphaFold monomer V2.0 prediction for U6 snrna-associated sm-like protein LSM5 (P40089) · a predicted model of the same protein · chain E 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 P49960
Every structure of UniProt P38203
Every structure of UniProt P57743
Every structure of UniProt P40070
Every structure of UniProt P40089
Every structure of UniProt Q06406
Every structure of UniProt P53905
Every structure of UniProt P47093
Elsewhere: RCSB PDB 5VSU · PDBe 5VSU · UniProt P49960 · UniProt P38203 · UniProt P57743 · UniProt P40070 · UniProt P40089 · UniProt Q06406 · UniProt P53905 · UniProt P47093

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