MolNFT v1 · #143201 · protein + RNA

Structure of yeast U6 snrnp with 3'-phosphate terminated U6 RNA

6ASO · U4/U6 snrna-associated-splicing factor PRP24: “Structure of yeast U6 snrnp with 3'-phosphate terminated U6 RNA”. X-ray diffraction, 4 ligands (UBD, K, MG), 17 pockets (best druggability 0.75). MolNFT v1 #143201 on GenesisL1: 3D…

PDB: 6ASO
Type: protein + RNA
Length: 975 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, A6ZYX7, P53905, P47093
Ligands: UBD, K, MG, MN
Pockets: 17 · best druggability 0.75

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	369	37% helix, 29% strand	P49960
B	U6 snrna-associated sm-like protein LSM2	protein	95	27% helix, 35% strand	P38203
C	U6 snrna-associated sm-like protein LSM3	protein	79	11% helix, 57% strand	P57743
D	U6 snrna-associated sm-like protein LSM4	protein	59	15% helix, 44% strand	P40070
E	U6 snrna-associated sm-like protein LSM5	protein	79	11% helix, 52% strand	P40089
F	U6 snrna-associated sm-like protein LSM6	protein	75	13% helix, 52% strand	A6ZYX7
G	U6 snrna-associated sm-like protein LSM7	protein	67	10% helix, 58% strand	P53905
H	U6 snrna-associated sm-like protein LSM8	protein	83	16% helix, 37% strand	P47093
I	Saccharomyces cerevisiae strain HB_S_GIMBLETTROAD_9 chromosome XII sequence	rna	69	—	—

Ligands and binding sites

UBD · Uridine 3',5'-bis(dihydrogen phosphate) · ligand · chains B, C, F, H, I
K · Potassium ion · metal · 2 copies · chains A, I
MG · Magnesium ion · metal · 2 copies · chains I
MN · Manganese (II) ion · metal · chains I

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

Pockets

17 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	784	0.75	0.79	69	empty
2	939	0.72	0.76	78	UBD
3	1186	0.70	0.75	76	MN, MG
4	118	0.58	0.85	22	empty
5	130	0.56	0.83	24	K

Interfaces

19 interfaces between chains.

A–I · 2810 Å² buried · 86 hydrogen bonds · protein-nucleic
B–C · 1384 Å² buried · 22 hydrogen bonds · protein-protein
B–H · 1038 Å² buried · 16 hydrogen bonds · protein-protein
E–G · 991 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 820 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

6ASO · Structure of yeast U6 snRNP with 3'-phosphate terminated U6 RNA · the same entry in another collection · chain E against E, TM-score 1.00
P49960 · AlphaFold monomer V2.0 prediction for U4/U6 snrna-associated-splicing factor PRP24… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 0.97
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 0.97

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 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 A6ZYX7
Every structure of UniProt P53905
Every structure of UniProt P47093
Elsewhere: RCSB PDB 6ASO · PDBe 6ASO · UniProt P49960 · UniProt P38203 · UniProt P57743 · UniProt P40070 · UniProt P40089 · UniProt A6ZYX7 · UniProt P53905 · UniProt P47093

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