Research workbench

The crystal structure of a heptameric archaeal sm protein: implications for the eukaryotic snrnp core

Analyse The crystal structure of a heptameric archaeal sm protein: implications for the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1I8F
Type: protein
Length: 499 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative snrnp sm-like protein
UniProt: Q8ZYG5
Pockets: 5 · best druggability 0.52

Structure

x-ray diffraction · 7 distinct chains · 15% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative snrnp sm-like protein	protein	71	17% helix, 59% strand	Q8ZYG5
B	Putative snrnp sm-like protein	protein	72	14% helix, 58% strand	Q8ZYG5
C	Putative snrnp sm-like protein	protein	68	12% helix, 62% strand	Q8ZYG5
D	Putative snrnp sm-like protein	protein	73	18% helix, 58% strand	Q8ZYG5
E	Putative snrnp sm-like protein	protein	70	17% helix, 60% strand	Q8ZYG5
F	Putative snrnp sm-like protein	protein	77	17% helix, 55% strand	Q8ZYG5
G	Putative snrnp sm-like protein	protein	68	12% helix, 62% strand	Q8ZYG5

Ligands and binding sites

GOL · Glycerol · additive · 5 copies · chains A, B, C, D, E, F, G

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	324	0.52	0.74	30	empty
2	104	0.40	0.76	20	empty
3	86	0.35	0.75	18	empty
4	68	0.33	0.76	22	empty
5	57	0.27	0.74	14	empty

Interfaces

14 interfaces between chains.

B–C · 920 Å² buried · 18 hydrogen bonds · protein-protein
F–G · 920 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 891 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 887 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 858 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

1I8F · The crystal structure of a heptameric archaeal sm protein: implications for the… · the same entry in another collection · chain A against A, 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 Q8ZYG5
Elsewhere: RCSB PDB 1I8F · PDBe 1I8F · UniProt Q8ZYG5

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.