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Crystal structure of S. pombe smn yg-dimer

Analyse Crystal structure of S. pombe smn yg-dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4RG5
Type: protein
Length: 801 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Maltose-binding periplasmic protein, survival motor neuron protein chimera
UniProt: G4PNN1, Q09808
Ligands: GLC, SO4
Pockets: 8 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Maltose-binding periplasmic protein, survival motor neuron protein chimera	protein	401	49% helix, 18% strand	G4PNN1, Q09808
B	Maltose-binding periplasmic protein, survival motor neuron protein chimera	protein	400	49% helix, 19% strand	G4PNN1, Q09808

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 7 copies · chains A, B
MLI · Malonate ion · additive · 2 copies · chains B

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

Pockets

8 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	988	0.80	0.82	82	GLC
2	554	0.75	0.82	53	GLC
3	197	0.62	0.83	34	empty
4	59	0.40	0.81	14	empty
5	56	0.38	0.80	17	empty

Interfaces

1 interface between chains.

A–B · 1918 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

4RG5 · Crystal Structure of S. Pombe SMN YG-Dimer · the same entry in another collection · chain A against A, TM-score 1.00
Q09808 · AlphaFold monomer V2.0 prediction for survival motor neuron-like protein 1 (Q09808) · a predicted model of the same protein · chain B against A, TM-score 0.11

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 G4PNN1
Every structure of UniProt Q09808
Elsewhere: RCSB PDB 4RG5 · PDBe 4RG5 · UniProt G4PNN1 · UniProt Q09808

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