MolNFT v1 · #166914 · protein + RNA

Cryo-EM structure of an active human histone pre-mRNA 3'-end processing machinery at 3.2 ångström resolution

6V4X · Small nuclear ribonucleoprotein sm D3: “Cryo-EM structure of an active human histone pre-mRNA 3'-end processing machinery at 3.2 ångström resolution”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.84). MolNFT…

PDB: 6V4X
Type: protein + RNA
Length: 1,983 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Small nuclear ribonucleoprotein sm D3; Small nuclear ribonucleoprotein-associated…
EC: 3.1.27.-
UniProt: P62318, P14678, P62306, P62304, P62308, Q969L4, P83369, Q9UKF6, Q9P2I0, Q92797
Ligands: ZN
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 12 distinct chains · 29% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Small nuclear ribonucleoprotein sm D3	protein	83	16% helix, 46% strand	P62318
B	Small nuclear ribonucleoprotein-associated proteins B and B'	protein	76	9% helix, 47% strand	P14678
F	Small nuclear ribonucleoprotein F	protein	74	12% helix, 58% strand	P62306
E	Small nuclear ribonucleoprotein E	protein	81	17% helix, 43% strand	P62304
G	Small nuclear ribonucleoprotein G	protein	77	12% helix, 45% strand	P62308
C	U7 snrna-associated sm-like protein LSM10	protein	114	25% helix, 21% strand	Q969L4
D	U7 snrna-associated sm-like protein LSM11	protein	106	13% helix, 38% strand	P83369
H	Cleavage and polyadenylation specificity factor subunit 3 (EC 3.1.27.-)	protein	499	25% helix, 22% strand	Q9UKF6
I	Cleavage and polyadenylation specificity factor subunit 2	protein	510	24% helix, 20% strand	Q9P2I0
J	Symplekin	protein	311	70% helix, 0% strand	Q92797
Z	U7 snrna	rna	27	—	—
Y	Modified H2A pre-mRNA	rna	25	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains H, 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, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	544	0.84	0.90	67	empty
2	926	0.77	0.81	69	empty
3	978	0.77	0.79	105	empty
4	263	0.76	0.90	45	empty
5	454	0.76	0.85	45	empty

Interfaces

34 interfaces between chains.

H–I · 2673 Å² buried · 28 hydrogen bonds · protein-protein
H–Y · 1543 Å² buried · 30 hydrogen bonds · protein-nucleic
C–D · 1278 Å² buried · 19 hydrogen bonds · protein-protein
E–G · 1064 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 952 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6V4X · Cryo-EM structure of an active human histone pre-mRNA 3'-end processing machinery at 3.2… · the same entry in another collection · chain Y against Y, 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 P62318
Every structure of UniProt P14678
Every structure of UniProt P62306
Every structure of UniProt P62304
Every structure of UniProt P62308
Every structure of UniProt Q969L4
Every structure of UniProt P83369
Every structure of UniProt Q9UKF6
Every structure of UniProt Q9P2I0
Every structure of UniProt Q92797
Elsewhere: RCSB PDB 6V4X · PDBe 6V4X · UniProt P62318 · UniProt P14678 · UniProt P62306 · UniProt P62304 · UniProt P62308 · UniProt Q969L4 · UniProt P83369 · UniProt Q9UKF6 · UniProt Q9P2I0 · UniProt Q92797

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