MolNFT v1 · #170360 · protein + RNA

5'DOMAIN of human 17S U2 snrnp

6Y50 · Splicing factor 3A subunit 3: “5'DOMAIN of human 17S U2 snrnp”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.85). MolNFT v1 #170360 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6Y50
Type: protein + RNA
Length: 2,587 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Splicing factor 3A subunit 3; Phd finger-like domain-containing protein 5A; Splicing…
EC: 3.6.4.13
UniProt: Q12874, Q7RTV0, Q9BWJ5, Q13435, Q15393, O75533, O43719, Q7L014
Ligands: ZN
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 9 distinct chains · 33% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
9	Splicing factor 3A subunit 3	protein	107	36% helix, 6% strand	Q12874
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	107	25% helix, 0% strand	Q13435
v	Splicing factor 3B subunit 3	protein	1177	7% helix, 39% strand	Q15393
u	Splicing factor 3B subunit 1	protein	842	70% helix, 0% strand	O75533
2	U2 snrna	rna	50	—	—
q	HIV tat-specific factor 1	protein	94	20% helix, 18% strand	O43719
p	Probable ATP-dependent RNA helicase DDX46 (EC 3.6.4.13)	protein	51	67% helix, 0% strand	Q7L014

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains y

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	1196	0.85	0.86	156	empty
2	816	0.83	0.86	128	empty
3	522	0.83	0.90	107	empty
4	933	0.83	0.84	133	empty
5	943	0.80	0.82	75	empty

Interfaces

16 interfaces between chains.

x–v · 1838 Å² buried · 18 hydrogen bonds · protein-protein
8–u · 1395 Å² buried · 7 hydrogen bonds · protein-protein
x–u · 1154 Å² buried · 13 hydrogen bonds · protein-protein
v–u · 1152 Å² buried · 2 hydrogen bonds · protein-protein
y–u · 518 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6Y50 · 5'domain of human 17S U2 snRNP · the same entry in another collection · chain p against p, TM-score 1.00
Q15393 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 3 (Q15393) · a predicted model of the same protein · chain v against A, TM-score 0.97
Q13435 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 2 (Q13435) · a predicted model of the same protein · chain 8 against A, TM-score 0.89
Q7RTV0 · AlphaFold monomer V2.0 prediction for phd finger-like domain- containing protein 5A… · a predicted model of the same protein · chain y against A, TM-score 0.87

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 Q12874
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 O43719
Every structure of UniProt Q7L014
Elsewhere: RCSB PDB 6Y50 · PDBe 6Y50 · UniProt Q12874 · UniProt Q7RTV0 · UniProt Q9BWJ5 · UniProt Q13435 · UniProt Q15393 · UniProt O75533 · UniProt O43719 · UniProt Q7L014

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