MolNFT v1 · #157713 · protein + RNA

S. cerevisiae U1 snrnp

6N7X · U1 small nuclear ribonucleoprotein 70 kda homolog: “S. cerevisiae U1 snrnp”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #157713 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6N7X
Type: protein + RNA
Length: 3,039 residues
Chains: 16
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U1 small nuclear ribonucleoprotein 70 kda homolog; U1 small nuclear ribonucleoprotein C…
UniProt: Q00916, Q05900, P32605, Q03776, P39682, Q00539, Q03782, P53207, P40018, Q02260, Q06217, P43321, Q12330, P54999, P40204
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 16 distinct chains · 44% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	U1 small nuclear ribonucleoprotein 70 kda homolog	protein	186	33% helix, 17% strand	Q00916
B	U1 small nuclear ribonucleoprotein C	protein	176	39% helix, 4% strand	Q05900
C	U1 small nuclear ribonucleoprotein a	protein	131	33% helix, 15% strand	P32605
D	U1 small nuclear ribonucleoprotein component PRP42	protein	539	69% helix, 0% strand	Q03776
E	Pre-mRNA-processing factor 39	protein	583	64% helix, 1% strand	P39682
F	Protein NAM8	protein	187	28% helix, 11% strand	Q00539
G	56 kda U1 small nuclear ribonucleoprotein component	protein	229	48% helix, 18% strand	Q03782
H	U1 small nuclear ribonucleoprotein component SNU71	protein	52	38% helix, 15% strand	P53207
K	Small nuclear ribonucleoprotein-associated protein B	protein	124	26% helix, 27% strand	P40018
L	Small nuclear ribonucleoprotein sm D1	protein	119	23% helix, 30% strand	Q02260
M	Small nuclear ribonucleoprotein sm D2	protein	96	22% helix, 48% strand	Q06217
N	Small nuclear ribonucleoprotein sm D3	protein	92	21% helix, 38% strand	P43321
O	Small nuclear ribonucleoprotein E	protein	74	12% helix, 47% strand	Q12330
P	Small nuclear ribonucleoprotein F	protein	68	10% helix, 53% strand	P54999
Q	Small nuclear ribonucleoprotein G	protein	75	0% helix, 49% strand	P40204
R	U1 snrna	rna	308	—	—

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	672	0.85	0.89	65	empty
2	745	0.84	0.87	98	empty
3	1191	0.82	0.83	100	empty
4	1173	0.81	0.83	84	empty
5	442	0.81	0.88	57	empty

Interfaces

49 interfaces between chains.

D–E · 3674 Å² buried · 17 hydrogen bonds · protein-protein
B–D · 3051 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 2227 Å² buried · 22 hydrogen bonds · protein-protein
D–G · 2118 Å² buried · 10 hydrogen bonds · protein-protein
B–R · 2106 Å² buried · 28 hydrogen bonds · protein-nucleic

Compared structures

6N7X · S. cerevisiae U1 snRNP · the same entry in another collection · chain M against M, 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 Q00916
Every structure of UniProt Q05900
Every structure of UniProt P32605
Every structure of UniProt Q03776
Every structure of UniProt P39682
Every structure of UniProt Q00539
Every structure of UniProt Q03782
Every structure of UniProt P53207
Every structure of UniProt P40018
Every structure of UniProt Q02260
Every structure of UniProt Q06217
Every structure of UniProt P43321
Every structure of UniProt Q12330
Every structure of UniProt P54999
Every structure of UniProt P40204
Elsewhere: RCSB PDB 6N7X · PDBe 6N7X · UniProt Q00916 · UniProt Q05900 · UniProt P32605 · UniProt Q03776 · UniProt P39682 · UniProt Q00539 · UniProt Q03782 · UniProt P53207 · UniProt P40018 · UniProt Q02260 · UniProt Q06217 · UniProt P43321 · UniProt Q12330 · UniProt P54999 · UniProt P40204

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