MolNFT v1 · #170383 · protein + RNA

Human 17S U2 snrnp

6Y5Q · Phd finger-like domain-containing protein 5A: “Human 17S U2 snrnp”. Electron microscopy, 20 pockets (best druggability 0.75). MolNFT v1 #170383 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6Y5Q
Type: protein + RNA
Length: 4,911 residues
Chains: 22
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phd finger-like domain-containing protein 5A; Splicing factor 3B subunit 5; Splicing…
EC: 3.6.4.13
UniProt: Q7RTV0, Q9BWJ5, Q13435, Q15393, O75533, Q7L014, P09661, P08579, Q9Y3B4, Q15459, Q15428, Q12874, Q15427, P14678, P62308, P62314, P62316, P62318, P62304, P62306, O43719
Pockets: 20 · best druggability 0.75

Structure

electron microscopy · 22 distinct chains · 31% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
y	Phd finger-like domain-containing protein 5A	protein	93	11% helix, 16% strand	Q7RTV0
x	Splicing factor 3B subunit 5	protein	66	53% helix, 0% strand	Q9BWJ5
8	Splicing factor 3B subunit 2	protein	172	24% helix, 5% strand	Q13435
v	Splicing factor 3B subunit 3	protein	1177	7% helix, 39% strand	Q15393
u	Splicing factor 3B subunit 1	protein	863	69% helix, 0% strand	O75533
p	Probable ATP-dependent RNA helicase DDX46 (EC 3.6.4.13)	protein	445	42% helix, 13% strand	Q7L014
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
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	420	53% helix, 3% 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	178	25% helix, 23% strand	O43719
2	U2SNRNA	rna	148	—	—

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	939	0.75	0.79	120	empty
2	916	0.75	0.79	97	empty
3	848	0.74	0.79	119	empty
4	818	0.72	0.78	90	empty
5	685	0.72	0.80	98	empty

Interfaces

40 interfaces between chains.

h–2 · 634 Å² buried · 18 hydrogen bonds · protein-nucleic
8–u · 546 Å² buried · 1 hydrogen bond · protein-protein
b–2 · 472 Å² buried · 10 hydrogen bonds · protein-nucleic
v–u · 376 Å² buried · 1 hydrogen bond · protein-protein
l–2 · 371 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

6Y5Q · human 17S U2 snRNP · the same entry in another collection · chain 7 against 7, 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 Q7RTV0
Every structure of UniProt Q9BWJ5
Every structure of UniProt Q13435
Every structure of UniProt Q15393
Every structure of UniProt O75533
Every structure of UniProt Q7L014
Every structure of UniProt P09661
Every structure of UniProt P08579
Every structure of UniProt Q9Y3B4
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
Elsewhere: RCSB PDB 6Y5Q · PDBe 6Y5Q · UniProt Q7RTV0 · UniProt Q9BWJ5 · UniProt Q13435 · UniProt Q15393 · UniProt O75533 · UniProt Q7L014 · UniProt P09661 · UniProt P08579 · UniProt Q9Y3B4 · UniProt Q15459 · UniProt Q15428 · UniProt Q12874 · UniProt Q15427 · UniProt P14678 · UniProt P62308 · UniProt P62314 · UniProt P62316 · UniProt P62318 · UniProt P62304 · UniProt P62306 · UniProt O43719

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