MolNFT v1 · #172539 · protein + RNA

Human C complex spliceosome - medium-resolution periphery

7A5P · U2 snrna: “Human C complex spliceosome - medium-resolution periphery”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #172539 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7A5P
Type: protein + RNA
Length: 9,876 residues
Chains: 48
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U2 snrna; U5 snrna; U6 snrna; Unknown; Pre-mRNA-processing-splicing factor 8; Snw…
EC: 2.3.2.27, 3.6.4.13, 5.2.1.8
UniProt: Q6P2Q9, Q13573, O60508, Q9UMS4, O75934, Q99459, Q9HCS7, O95926, Q9BZJ0, Q9NW64, Q9UQ35, Q9HCG8, O60306, P09661, P08579, P62318, P14678, P62314, P62316, P62304, P62306, P62308, Q9UNP9, Q9NW82, O75643, Q92620, Q9ULR0, Q9BW85, P61326, Q9Y5S9, Q14331, P38919, Q96BP3
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 48 distinct chains · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	U2 snrna	rna	155	—	—
5	U5 snrna	rna	40	—	—
6	U6 snrna	rna	16	—	—
8	Unknown	protein	76	79% helix, 0% strand	—
A	Pre-mRNA-processing-splicing factor 8	protein	491	26% helix, 18% strand	Q6P2Q9
C	Snw domain-containing protein 1	protein	15	87% helix, 0% strand	Q13573
E	Pre-mRNA-processing factor 17	protein	305	0% helix, 45% strand	O60508
G	Pre-mRNA-processing factor 19 (EC 2.3.2.27)	protein	132	53% helix, 5% strand	Q9UMS4
H	Pre-mRNA-processing factor 19 (EC 2.3.2.27)	protein	135	53% helix, 1% strand	Q9UMS4
I	Pre-mRNA-processing factor 19 (EC 2.3.2.27)	protein	133	56% helix, 5% strand	Q9UMS4
J	Pre-mRNA-processing factor 19 (EC 2.3.2.27)	protein	110	66% helix, 2% strand	Q9UMS4
K	Pre-mRNA-splicing factor SPF27	protein	138	81% helix, 0% strand	O75934
L	Cell division cycle 5-like protein	protein	115	86% helix, 0% strand	Q99459
M	Pre-mRNA-splicing factor SYF1	protein	672	63% helix, 0% strand	Q9HCS7
N	Pre-mRNA-splicing factor SYF2	protein	73	49% helix, 0% strand	O95926
O	Crooked neck-like protein 1	protein	261	62% helix, 0% strand	Q9BZJ0
P	Pre-mRNA-splicing factor RBM22	protein	90	14% helix, 16% strand	Q9NW64
S	SERINE/ARGININE repetitive matrix protein 2	protein	46	87% helix, 0% strand	Q9UQ35
T	Pre-mRNA-splicing factor CWC22 homolog	protein	253	71% helix, 1% strand	Q9HCG8
U	Intron-binding protein aquarius (EC 3.6.4.13)	protein	1293	49% helix, 12% strand	O60306
W	U2 small nuclear ribonucleoprotein a'	protein	174	30% helix, 16% strand	P09661
X	U2 small nuclear ribonucleoprotein B''	protein	93	33% helix, 25% strand	P08579
Y	Pre-mRNA	rna	29	—	—
a	Small nuclear ribonucleoprotein sm D3	protein	72	11% helix, 54% strand	P62318
b	Small nuclear ribonucleoprotein-associated proteins B and B'	protein	66	5% helix, 61% strand	P14678
c	Small nuclear ribonucleoprotein sm D1	protein	81	16% helix, 46% strand	P62314
d	Small nuclear ribonucleoprotein sm D2	protein	81	22% helix, 48% strand	P62316
e	Small nuclear ribonucleoprotein E	protein	79	18% helix, 54% strand	P62304
f	Small nuclear ribonucleoprotein F	protein	74	14% helix, 57% strand	P62306
g	Small nuclear ribonucleoprotein G	protein	74	12% helix, 53% strand	P62308
h	Small nuclear ribonucleoprotein sm D2	protein	84	23% helix, 49% strand	P62316
i	Small nuclear ribonucleoprotein F	protein	71	14% helix, 59% strand	P62306
j	Small nuclear ribonucleoprotein E	protein	78	18% helix, 55% strand	P62304
k	Small nuclear ribonucleoprotein G	protein	73	8% helix, 55% strand	P62308
l	Small nuclear ribonucleoprotein sm D3	protein	83	17% helix, 47% strand	P62318
m	Small nuclear ribonucleoprotein-associated proteins B and B'	protein	70	10% helix, 57% strand	P14678
n	Small nuclear ribonucleoprotein sm D1	protein	82	13% helix, 45% strand	P62314
o	Peptidyl-prolyl cis-trans isomerase E (EC 5.2.1.8)	protein	77	29% helix, 35% strand	Q9UNP9
p	Wd repeat-containing protein 70	protein	68	35% helix, 0% strand	Q9NW82
q	U5 small nuclear ribonucleoprotein 200 kda helicase (EC 3.6.4.13)	protein	1896	43% helix, 16% strand	O75643
r	Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 (EC 3.6.4.13)	protein	593	41% helix, 19% strand	Q92620
s	Pre-mRNA-splicing factor ISY1 homolog	protein	76	80% helix, 0% strand	Q9ULR0
u	Splicing factor YJU2	protein	43	81% helix, 0% strand	Q9BW85
v	Protein mago nashi homolog	protein	144	36% helix, 34% strand	P61326
w	RNA-binding protein 8A	protein	91	24% helix, 35% strand	Q9Y5S9
x	Protein FRG1	protein	125	0% helix, 42% strand	Q14331
y	Eukaryotic initiation factor 4A-III (EC 3.6.4.13)	protein	390	41% helix, 17% strand	P38919
z	Peptidylprolyl isomerase domain and wd repeat-containing protein 1 (EC 5.2.1.8)	protein	460	5% helix, 45% strand	Q96BP3

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	1031	0.86	0.87	173	empty
2	928	0.85	0.87	163	empty
3	814	0.84	0.87	112	empty
4	1015	0.84	0.85	161	empty
5	1184	0.83	0.84	172	empty

Interfaces

82 interfaces between chains.

2–X · 881 Å² buried · 14 hydrogen bonds · protein-nucleic
I–J · 774 Å² buried · 2 hydrogen bonds · protein-protein
K–L · 756 Å² buried · 0 hydrogen bonds · protein-protein
G–I · 729 Å² buried · 2 hydrogen bonds · protein-protein
2–6 · 616 Å² buried · 48 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 34 modified (engineered).

Compared structures

7A5P · Human C Complex Spliceosome - Medium-resolution PERIPHERY · the same entry in another collection · chain J against J, 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 Q6P2Q9
Every structure of UniProt Q13573
Every structure of UniProt O60508
Every structure of UniProt Q9UMS4
Every structure of UniProt O75934
Every structure of UniProt Q99459
Every structure of UniProt Q9HCS7
Every structure of UniProt O95926
Every structure of UniProt Q9BZJ0
Every structure of UniProt Q9NW64
Every structure of UniProt Q9UQ35
Every structure of UniProt Q9HCG8
Every structure of UniProt O60306
Every structure of UniProt P09661
Every structure of UniProt P08579
Every structure of UniProt P62318
Every structure of UniProt P14678
Every structure of UniProt P62314
Every structure of UniProt P62316
Every structure of UniProt P62304
Every structure of UniProt P62306
Every structure of UniProt P62308
Every structure of UniProt Q9UNP9
Every structure of UniProt Q9NW82
Every structure of UniProt O75643
Every structure of UniProt Q92620
Every structure of UniProt Q9ULR0
Every structure of UniProt Q9BW85
Every structure of UniProt P61326
Every structure of UniProt Q9Y5S9
Every structure of UniProt Q14331
Every structure of UniProt P38919
Every structure of UniProt Q96BP3
Elsewhere: RCSB PDB 7A5P · PDBe 7A5P · UniProt Q6P2Q9 · UniProt Q13573 · UniProt O60508 · UniProt Q9UMS4 · UniProt O75934 · UniProt Q99459 · UniProt Q9HCS7 · UniProt O95926 · UniProt Q9BZJ0 · UniProt Q9NW64 · UniProt Q9UQ35 · UniProt Q9HCG8 · UniProt O60306 · UniProt P09661 · UniProt P08579 · UniProt P62318 · UniProt P14678 · UniProt P62314 · UniProt P62316 · UniProt P62304 · UniProt P62306 · UniProt P62308 · UniProt Q9UNP9 · UniProt Q9NW82 · UniProt O75643 · UniProt Q92620 · UniProt Q9ULR0 · UniProt Q9BW85 · UniProt P61326 · UniProt Q9Y5S9 · UniProt Q14331 · UniProt P38919 · UniProt Q96BP3

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