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Structure of the LSM657 complex: an assembly intermediate of the LSM1 7 and LSM2 8 rings

Analyse Structure of the LSM657 complex: an assembly intermediate of the LSM1 7 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SWN
Type: protein
Length: 874 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U6 snrna-associated sm-like protein LSM7; U6 snrna-associated sm-like protein LSM5; U6…
UniProt: O74499, O42978, Q9UUI1
Ligands: ZN
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 10 distinct chains · 9% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	U6 snrna-associated sm-like protein LSM7	protein	68	0% helix, 57% strand	O74499
A, P	U6 snrna-associated sm-like protein LSM5	protein	76	9% helix, 54% strand	O42978
B	U6 snrna-associated sm-like protein LSM6	protein	71	13% helix, 55% strand	Q9UUI1
F	U6 snrna-associated sm-like protein LSM7	protein	78	6% helix, 58% strand	O74499
D	U6 snrna-associated sm-like protein LSM5	protein	73	12% helix, 56% strand	O42978
E, T	U6 snrna-associated sm-like protein LSM6	protein	72	14% helix, 58% strand	Q9UUI1
O	U6 snrna-associated sm-like protein LSM7	protein	67	4% helix, 58% strand	O74499
Q	U6 snrna-associated sm-like protein LSM6	protein	73	12% helix, 52% strand	Q9UUI1
R	U6 snrna-associated sm-like protein LSM7	protein	76	7% helix, 58% strand	O74499
S	U6 snrna-associated sm-like protein LSM5	protein	72	13% helix, 57% strand	O42978

Ligands and binding sites

ZN · Zinc ion · metal · 16 copies · chains C, A, B, F, D, E, O, P, Q, R, S, T

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 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	848	0.75	0.80	103	empty
2	856	0.73	0.78	78	empty
3	233	0.60	0.80	31	empty
4	132	0.42	0.76	19	empty
5	67	0.40	0.80	14	empty

Interfaces

14 interfaces between chains.

O–P · 962 Å² buried · 13 hydrogen bonds · protein-protein
C–A · 955 Å² buried · 13 hydrogen bonds · protein-protein
F–D · 930 Å² buried · 11 hydrogen bonds · protein-protein
R–S · 891 Å² buried · 11 hydrogen bonds · protein-protein
Q–R · 844 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3SWN · Structure of the LSm657 Complex: An Assembly Intermediate of the LSm1 7 and LSm2 8 Rings · the same entry in another collection · chain T against T, 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 O74499
Every structure of UniProt O42978
Every structure of UniProt Q9UUI1
Elsewhere: RCSB PDB 3SWN · PDBe 3SWN · UniProt O74499 · UniProt O42978 · UniProt Q9UUI1

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