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Crystal structure of LSM2-8 complex bound to the RNA fragment cguuu

Analyse Crystal structure of LSM2-8 complex bound to the RNA fragment cguuu in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4M7D
Type: protein + RNA
Length: 1,048 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U6 snrna-associated sm-like protein LSM8; U6 snrna-associated sm-like protein LSM2; U6…
UniProt: P47093, P38203, P57743, Q06406, P40089, P53905, P40070
Pockets: 10 · best druggability 0.64

Structure

x-ray diffraction · 15 distinct chains · 13% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	U6 snrna-associated sm-like protein LSM8	protein	65	9% helix, 58% strand	P47093
B	U6 snrna-associated sm-like protein LSM2	protein	92	25% helix, 36% strand	P38203
C	U6 snrna-associated sm-like protein LSM3	protein	77	4% helix, 64% strand	P57743
D, K	U6 snrna-associated sm-like protein LSM6	protein	74	14% helix, 50% strand	Q06406
E	U6 snrna-associated sm-like protein LSM5	protein	77	13% helix, 49% strand	P40089
F	U6 snrna-associated sm-like protein LSM7	protein	66	6% helix, 53% strand	P53905
G	U6 snrna-associated sm-like protein LSM4	protein	77	18% helix, 49% strand	P40070
H	U6 snrna-associated sm-like protein LSM8	protein	64	5% helix, 55% strand	P47093
I	U6 snrna-associated sm-like protein LSM2	protein	88	26% helix, 36% strand	P38203
J	U6 snrna-associated sm-like protein LSM3	protein	78	12% helix, 63% strand	P57743
L	U6 snrna-associated sm-like protein LSM5	protein	76	13% helix, 55% strand	P40089
M	U6 snrna-associated sm-like protein LSM7	protein	65	6% helix, 46% strand	P53905
N	U6 snrna-associated sm-like protein LSM4	protein	66	11% helix, 52% strand	P40070
O	U6 snrna	rna	5	—	—
P	U6 snrna	rna	4	—	—

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	704	0.64	0.74	67	empty
2	674	0.64	0.74	63	empty
3	284	0.60	0.79	35	empty
4	163	0.44	0.75	23	empty
5	69	0.37	0.78	16	empty

Interfaces

30 interfaces between chains.

B–C · 1349 Å² buried · 19 hydrogen bonds · protein-protein
I–J · 1297 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 934 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 922 Å² buried · 11 hydrogen bonds · protein-protein
H–I · 918 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4M7D · Crystal structure of Lsm2-8 complex bound to the RNA fragment CGUUU · the same entry in another collection · chain J against J, 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 P47093
Every structure of UniProt P38203
Every structure of UniProt P57743
Every structure of UniProt Q06406
Every structure of UniProt P40089
Every structure of UniProt P53905
Every structure of UniProt P40070
Elsewhere: RCSB PDB 4M7D · PDBe 4M7D · UniProt P47093 · UniProt P38203 · UniProt P57743 · UniProt Q06406 · UniProt P40089 · UniProt P53905 · UniProt P40070

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