MolNFT v1 · #125775 · protein + RNA

Structure of the core of the yeast spliceosome immediately after branching

5LJ3 · U5 snrna (small nuclear RNA): “Structure of the core of the yeast spliceosome immediately after branching”. Electron microscopy, 3 ligands (GTP, ZN, MG), 20 pockets (best druggability 0.89). MolNFT v1 #125775 on GenesisL1: 3D…

PDB: 5LJ3
Type: protein + RNA
Length: 7,895 residues
Chains: 38
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U5 snrna (small nuclear RNA); Exon 1 (5' exon) of UBC4 pre-mRNA; Intron of UBC4 pre-mRNA…
UniProt: P33334, P28320, P53854, P36048, A0A165UGV0, A0A162ERE7, A0A162HKW4, P28004, P25337, A0A162HWE4, P38241, A0A165TLN2, A0A162GIZ3, Q03375, A0A165TU20, A0A165VVY6, P40018, P43321, Q12330, P54999, P40204, Q02260, Q06217, Q08963, P40567
Ligands: GTP, ZN, MG
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 32 distinct chains · 46% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
U	U5 snrna (small nuclear RNA)	rna	141	—	—
E	Exon 1 (5' exon) of UBC4 pre-mRNA	rna	16	—	—
I	Intron of UBC4 pre-mRNA	rna	33	—	—
Z	U2 snrna (small nuclear RNA)	rna	171	—	—
V	U6 snrna (small nuclear RNA)	rna	97	—	—
A	Pre-mRNA-splicing factor 8	protein	1922	45% helix, 10% strand	P33334
D	Protein CWC16	protein	114	11% helix, 32% strand	P28320
F	Pre-mRNA-splicing factor CWC25	protein	46	74% helix, 0% strand	P53854
C	Pre-mRNA-splicing factor SNU114	protein	882	36% helix, 17% strand	P36048
G	ISY1	protein	97	60% helix, 1% strand	A0A165UGV0
H	CWC22	protein	399	74% helix, 0% strand	A0A162ERE7
J	PRP46	protein	326	3% helix, 42% strand	A0A162HKW4
K	Pre-mRNA-processing protein 45	protein	163	39% helix, 6% strand	P28004
L	Pre-mRNA-splicing factor BUD31	protein	155	52% helix, 0% strand	P25337
M	CWC2	protein	252	33% helix, 14% strand	A0A162HWE4
N	Pre-mRNA-splicing factor SLT11	protein	209	41% helix, 14% strand	P38241
O	CEF1	protein	198	61% helix, 0% strand	A0A165TLN2
P	CWC15	protein	36	0% helix, 0% strand	A0A162GIZ3
R	Pre-mRNA-splicing factor CWC21	protein	97	61% helix, 2% strand	Q03375
S	CLF1	protein	464	82% helix, 0% strand	A0A165TU20
T	SYF1	protein	592	80% helix, 0% strand	A0A165VVY6
b, k	Small nuclear ribonucleoprotein-associated protein B	protein	80	4% helix, 53% strand	P40018
d, n	Small nuclear ribonucleoprotein sm D3	protein	82	16% helix, 46% strand	P43321
e, p	Small nuclear ribonucleoprotein E	protein	75	19% helix, 36% strand	Q12330
f, q	Small nuclear ribonucleoprotein F	protein	72	10% helix, 53% strand	P54999
g, r	Small nuclear ribonucleoprotein G	protein	69	0% helix, 48% strand	P40204
h	Small nuclear ribonucleoprotein sm D1	protein	82	15% helix, 48% strand	Q02260
j, m	Small nuclear ribonucleoprotein sm D2	protein	94	23% helix, 39% strand	Q06217
W	U2 small nuclear ribonucleoprotein a'	protein	164	21% helix, 5% strand	Q08963
Y	U2 small nuclear ribonucleoprotein B''	protein	84	26% helix, 18% strand	P40567
l	Small nuclear ribonucleoprotein sm D1	protein	79	8% helix, 8% strand	Q02260
x	Unknown	protein	132	92% helix, 0% strand	—

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains C
ZN · Zinc ion · metal · 7 copies · chains D, L, V, M, N
MG · Magnesium ion · metal · 2 copies · chains E, I, V

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

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	840	0.89	0.92	102	empty
2	1077	0.89	0.90	110	GTP
3	1055	0.87	0.88	83	empty
4	1112	0.86	0.87	117	empty
5	469	0.86	0.93	74	empty

Interfaces

133 interfaces between chains.

A–C · 4801 Å² buried · 44 hydrogen bonds · protein-protein
U–A · 3959 Å² buried · 71 hydrogen bonds · protein-nucleic
A–K · 2199 Å² buried · 11 hydrogen bonds · protein-protein
Z–A · 1997 Å² buried · 44 hydrogen bonds · protein-nucleic
A–H · 1910 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5LJ3 · Structure of the core of the yeast spliceosome immediately after branching · the same entry in another collection · chain Z against Z, TM-score 1.00

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 P33334
Every structure of UniProt P28320
Every structure of UniProt P53854
Every structure of UniProt P36048
Every structure of UniProt A0A165UGV0
Every structure of UniProt A0A162ERE7
Every structure of UniProt A0A162HKW4
Every structure of UniProt P28004
Every structure of UniProt P25337
Every structure of UniProt A0A162HWE4
Every structure of UniProt P38241
Every structure of UniProt A0A165TLN2
Every structure of UniProt A0A162GIZ3
Every structure of UniProt Q03375
Every structure of UniProt A0A165TU20
Every structure of UniProt A0A165VVY6
Every structure of UniProt P40018
Every structure of UniProt P43321
Every structure of UniProt Q12330
Every structure of UniProt P54999
Every structure of UniProt P40204
Every structure of UniProt Q02260
Every structure of UniProt Q06217
Every structure of UniProt Q08963
Every structure of UniProt P40567
Elsewhere: RCSB PDB 5LJ3 · PDBe 5LJ3 · UniProt P33334 · UniProt P28320 · UniProt P53854 · UniProt P36048 · UniProt A0A165UGV0 · UniProt A0A162ERE7 · UniProt A0A162HKW4 · UniProt P28004 · UniProt P25337 · UniProt A0A162HWE4 · UniProt P38241 · UniProt A0A165TLN2 · UniProt A0A162GIZ3 · UniProt Q03375 · UniProt A0A165TU20 · UniProt A0A165VVY6 · UniProt P40018 · UniProt P43321 · UniProt Q12330 · UniProt P54999 · UniProt P40204 · UniProt Q02260 · UniProt Q06217 · UniProt Q08963 · UniProt P40567

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