MolNFT v1 · #99564 · protein

Crystal structure of LSM1-7 complex

4M75 · U6 snrna-associated sm-like protein LSM1: “Crystal structure of LSM1-7 complex”. X-ray diffraction, 1 ligand (CL), 12 pockets (best druggability 0.78). MolNFT v1 #99564 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4M75
Type: protein
Length: 1,189 residues
Chains: 14
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U6 snrna-associated sm-like protein LSM1; U6 snrna-associated sm-like protein LSM2; U6…
UniProt: P47017, P38203, P57743, Q06406, P40089, P53905, P40070
Ligands: CL
Pockets: 12 · best druggability 0.78

Structure

x-ray diffraction · 14 distinct chains · 19% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	U6 snrna-associated sm-like protein LSM1	protein	139	26% helix, 32% strand	P47017
B	U6 snrna-associated sm-like protein LSM2	protein	91	25% helix, 33% strand	P38203
C	U6 snrna-associated sm-like protein LSM3	protein	70	13% helix, 61% strand	P57743
D	U6 snrna-associated sm-like protein LSM6	protein	72	7% helix, 49% strand	Q06406
E	U6 snrna-associated sm-like protein LSM5	protein	75	11% helix, 55% strand	P40089
F	U6 snrna-associated sm-like protein LSM7	protein	75	9% helix, 48% strand	P53905
G	U6 snrna-associated sm-like protein LSM4	protein	82	20% helix, 40% strand	P40070
H	U6 snrna-associated sm-like protein LSM1	protein	134	33% helix, 34% strand	P47017
I	U6 snrna-associated sm-like protein LSM2	protein	86	30% helix, 38% strand	P38203
J	U6 snrna-associated sm-like protein LSM3	protein	75	12% helix, 56% strand	P57743
K	U6 snrna-associated sm-like protein LSM6	protein	71	15% helix, 46% strand	Q06406
L	U6 snrna-associated sm-like protein LSM5	protein	75	9% helix, 57% strand	P40089
M	U6 snrna-associated sm-like protein LSM7	protein	62	11% helix, 55% strand	P53905
N	U6 snrna-associated sm-like protein LSM4	protein	82	17% helix, 39% strand	P40070

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains B, C

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1183	0.78	0.80	104	empty
2	825	0.74	0.78	75	empty
3	642	0.72	0.79	63	empty
4	95	0.59	0.87	21	empty
5	195	0.51	0.77	32	empty

Interfaces

22 interfaces between chains.

A–B · 1348 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 1274 Å² buried · 21 hydrogen bonds · protein-protein
I–J · 1142 Å² buried · 16 hydrogen bonds · protein-protein
H–I · 1141 Å² buried · 14 hydrogen bonds · protein-protein
H–N · 1110 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 39 modified (engineered).

Compared structures

4M75 · Crystal structure of Lsm1-7 complex · the same entry in another collection · chain K against K, 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 P47017
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 4M75 · PDBe 4M75 · UniProt P47017 · UniProt P38203 · UniProt P57743 · UniProt Q06406 · UniProt P40089 · UniProt P53905 · UniProt P40070

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