MolNFT v1 · #170361 · protein + RNA

Human 17S U2 snrnp low resolution part

6Y53 · U2 small nuclear ribonucleoprotein a': “Human 17S U2 snrnp low resolution part”. Electron microscopy, 20 pockets (best druggability 0.73). MolNFT v1 #170361 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6Y53
Type: protein + RNA
Length: 2,324 residues
Chains: 19
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U2 small nuclear ribonucleoprotein a'; U2 small nuclear ribonucleoprotein B''; Splicing…
EC: 3.6.4.13
UniProt: P09661, P08579, Q9Y3B4, Q7L014, Q15459, Q15428, Q12874, Q15427, P14678, P62308, P62314, P62316, P62318, P62304, P62306, O43719, Q13435, O75533
Pockets: 20 · best druggability 0.73

Structure

electron microscopy · 19 distinct chains · 29% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a	U2 small nuclear ribonucleoprotein a'	protein	162	23% helix, 17% strand	P09661
b	U2 small nuclear ribonucleoprotein B''	protein	166	28% helix, 27% strand	P08579
z	Splicing factor 3B subunit 6	protein	77	23% helix, 22% strand	Q9Y3B4
p	Probable ATP-dependent RNA helicase DDX46 (EC 3.6.4.13)	protein	394	39% helix, 15% strand	Q7L014
6	Splicing factor 3A subunit 1	protein	123	59% helix, 0% strand	Q15459
7	Splicing factor 3A subunit 2	protein	100	4% helix, 33% strand	Q15428
9	Splicing factor 3A subunit 3	protein	313	58% helix, 2% strand	Q12874
o	Splicing factor 3B subunit 4	protein	160	23% helix, 29% strand	Q15427
m	Small nuclear ribonucleoprotein-associated proteins B and B'	protein	71	4% helix, 52% strand	P14678
k	Small nuclear ribonucleoprotein G	protein	74	0% helix, 50% strand	P62308
n	Small nuclear ribonucleoprotein sm D1	protein	82	12% helix, 46% strand	P62314
h	Small nuclear ribonucleoprotein sm D2	protein	98	16% helix, 45% strand	P62316
l	Small nuclear ribonucleoprotein sm D3	protein	83	10% helix, 43% strand	P62318
j	Small nuclear ribonucleoprotein E	protein	79	14% helix, 53% strand	P62304
i	Small nuclear ribonucleoprotein F	protein	74	9% helix, 58% strand	P62306
q	HIV tat-specific factor 1	protein	84	30% helix, 29% strand	O43719
8	Splicing factor 3B subunit 2	protein	65	22% helix, 14% strand	Q13435
u	Splicing factor 3B subunit 1	protein	21	33% helix, 10% strand	O75533
2	U2 snrna	rna	98	—	—

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	812	0.73	0.79	104	empty
2	680	0.72	0.80	98	empty
3	444	0.72	0.83	60	empty
4	649	0.72	0.80	70	empty
5	476	0.72	0.82	75	empty

Interfaces

23 interfaces between chains.

h–2 · 634 Å² buried · 18 hydrogen bonds · protein-nucleic
b–2 · 472 Å² buried · 10 hydrogen bonds · protein-nucleic
l–2 · 371 Å² buried · 8 hydrogen bonds · protein-nucleic
6–9 · 293 Å² buried · 0 hydrogen bonds · protein-protein
k–j · 269 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6Y53 · human 17S U2 snRNP low resolution part · the same entry in another collection · chain n against n, 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 P09661
Every structure of UniProt P08579
Every structure of UniProt Q9Y3B4
Every structure of UniProt Q7L014
Every structure of UniProt Q15459
Every structure of UniProt Q15428
Every structure of UniProt Q12874
Every structure of UniProt Q15427
Every structure of UniProt P14678
Every structure of UniProt P62308
Every structure of UniProt P62314
Every structure of UniProt P62316
Every structure of UniProt P62318
Every structure of UniProt P62304
Every structure of UniProt P62306
Every structure of UniProt O43719
Every structure of UniProt Q13435
Every structure of UniProt O75533
Elsewhere: RCSB PDB 6Y53 · PDBe 6Y53 · UniProt P09661 · UniProt P08579 · UniProt Q9Y3B4 · UniProt Q7L014 · UniProt Q15459 · UniProt Q15428 · UniProt Q12874 · UniProt Q15427 · UniProt P14678 · UniProt P62308 · UniProt P62314 · UniProt P62316 · UniProt P62318 · UniProt P62304 · UniProt P62306 · UniProt O43719 · UniProt Q13435 · UniProt O75533

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.