Research workbench

Saccharomyces cerevisiae spliceosomal pre-a complex (delta bs-a ACT1)

Analyse Saccharomyces cerevisiae spliceosomal pre-a complex (delta bs-a ACT1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7OQE
Type: protein + RNA
Length: 8,824 residues
Chains: 39
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein NAM8; ACT1 pre-mRNA (delta bs-a); U1 small nuclear ribonucleoprotein component…
UniProt: Q00539, Q03776, P53207, Q03782, P32605, Q05900, P40018, P43321, Q12330, P54999, P40204, Q02260, Q06217, Q07508, P39682, Q00916, P33203, P49955, Q07350, P32524, P19736, Q06835, Q02554, Q04693, Q99181, P0C074, Q08963, P40567, P21372
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 38 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F	Protein NAM8	protein	267	24% helix, 20% strand	Q00539
I	ACT1 pre-mRNA (delta bs-a)	rna	86	—	—
E	U1 small nuclear ribonucleoprotein component PRP42	protein	544	68% helix, 0% strand	Q03776
J	U1 small nuclear ribonucleoprotein component SNU71	protein	105	49% helix, 8% strand	P53207
1	U1 snrna	rna	558	—	—
G	56 kda U1 small nuclear ribonucleoprotein component	protein	239	44% helix, 15% strand	Q03782
A	U1 small nuclear ribonucleoprotein a	protein	132	34% helix, 16% strand	P32605
C	U1 small nuclear ribonucleoprotein C	protein	195	41% helix, 2% strand	Q05900
b	Small nuclear ribonucleoprotein-associated protein B	protein	121	26% helix, 31% strand	P40018
d	Small nuclear ribonucleoprotein sm D3	protein	93	19% helix, 40% strand	P43321
e	Small nuclear ribonucleoprotein E	protein	77	14% helix, 42% strand	Q12330
f, x	Small nuclear ribonucleoprotein F	protein	73	8% helix, 59% strand	P54999
g	Small nuclear ribonucleoprotein G	protein	72	4% helix, 50% strand	P40204
h	Small nuclear ribonucleoprotein sm D1	protein	107	24% helix, 35% strand	Q02260
i	Small nuclear ribonucleoprotein sm D2	protein	99	18% helix, 46% strand	Q06217
H	Protein LUC7	protein	192	65% helix, 3% strand	Q07508
D	Pre-mRNA-processing factor 39	protein	576	60% helix, 2% strand	P39682
B	U1 small nuclear ribonucleoprotein 70 kda homolog	protein	186	37% helix, 16% strand	Q00916
K	Pre-mRNA-processing protein PRP40	protein	406	68% helix, 0% strand	P33203
O	U2 snrnp component HSH155	protein	812	73% helix, 0% strand	P49955
U	Pre-mRNA-splicing factor PRP11	protein	188	17% helix, 23% strand	Q07350
V	Pre-mRNA-splicing factor PRP21	protein	103	63% helix, 0% strand	P32524
T	Pre-mRNA-splicing factor PRP9	protein	462	58% helix, 3% strand	P19736
S	Pre-mRNA-splicing factor RDS3	protein	92	17% helix, 16% strand	Q06835
Q	Cold sensitive U2 snrna suppressor 1	protein	220	35% helix, 5% strand	Q02554
P	Pre-mRNA-splicing factor RSE1	protein	1186	8% helix, 42% strand	Q04693
R	Protein HSH49	protein	173	29% helix, 32% strand	Q99181
Z	RDS3 complex subunit 10	protein	83	76% helix, 0% strand	P0C074
W	U2 small nuclear ribonucleoprotein a'	protein	170	22% helix, 13% strand	Q08963
Y	U2 small nuclear ribonucleoprotein B''	protein	84	26% helix, 23% strand	P40567
s	Small nuclear ribonucleoprotein-associated protein B	protein	65	0% helix, 52% strand	P40018
t	Small nuclear ribonucleoprotein sm D1	protein	72	13% helix, 54% strand	Q02260
u	Small nuclear ribonucleoprotein sm D2	protein	92	22% helix, 49% strand	Q06217
v	Small nuclear ribonucleoprotein sm D3	protein	82	16% helix, 46% strand	P43321
w	Small nuclear ribonucleoprotein E	protein	77	14% helix, 48% strand	Q12330
y	Small nuclear ribonucleoprotein G	protein	75	8% helix, 52% strand	P40204
p	Pre-mRNA-processing ATP-dependent RNA helicase PRP5	protein	444	46% helix, 15% strand	P21372
2	U2 snrna	rna	143	—	—

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	896	0.84	0.87	108	empty
2	625	0.84	0.89	89	empty
3	785	0.83	0.86	122	empty
4	495	0.82	0.89	108	empty
5	1170	0.82	0.83	116	empty

Interfaces

112 interfaces between chains.

1–A · 1247 Å² buried · 13 hydrogen bonds · protein-nucleic
1–C · 1210 Å² buried · 7 hydrogen bonds · protein-nucleic
E–D · 1120 Å² buried · 2 hydrogen bonds · protein-protein
O–Q · 1081 Å² buried · 0 hydrogen bonds · protein-protein
E–C · 797 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7OQE · Saccharomyces cerevisiae spliceosomal pre-A complex (delta BS-A ACT1) · the same entry in another collection · chain b against b, 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 Q00539
Every structure of UniProt Q03776
Every structure of UniProt P53207
Every structure of UniProt Q03782
Every structure of UniProt P32605
Every structure of UniProt Q05900
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 Q07508
Every structure of UniProt P39682
Every structure of UniProt Q00916
Every structure of UniProt P33203
Every structure of UniProt P49955
Every structure of UniProt Q07350
Every structure of UniProt P32524
Every structure of UniProt P19736
Every structure of UniProt Q06835
Every structure of UniProt Q02554
Every structure of UniProt Q04693
Every structure of UniProt Q99181
Every structure of UniProt P0C074
Every structure of UniProt Q08963
Every structure of UniProt P40567
Every structure of UniProt P21372
Elsewhere: RCSB PDB 7OQE · PDBe 7OQE · UniProt Q00539 · UniProt Q03776 · UniProt P53207 · UniProt Q03782 · UniProt P32605 · UniProt Q05900 · UniProt P40018 · UniProt P43321 · UniProt Q12330 · UniProt P54999 · UniProt P40204 · UniProt Q02260 · UniProt Q06217 · UniProt Q07508 · UniProt P39682 · UniProt Q00916 · UniProt P33203 · UniProt P49955 · UniProt Q07350 · UniProt P32524 · UniProt P19736 · UniProt Q06835 · UniProt Q02554 · UniProt Q04693 · UniProt Q99181 · UniProt P0C074 · UniProt Q08963 · UniProt P40567 · UniProt P21372

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