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Crystal structure of the GEMIN2-binding domain of smn, GEMIN2 in complex with SMD1(1-82)/D2/F/E/G from human

Analyse Crystal structure of the GEMIN2-binding domain of smn, GEMIN2 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XJQ
Type: protein
Length: 600 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gem-associated protein 2; Small nuclear ribonucleoprotein sm D1; Small nuclear…
UniProt: O14893, P62314, P62316, P62304, P62306, P62308, Q16637
Pockets: 8 · best druggability 0.60

Structure

x-ray diffraction · 7 distinct chains · 30% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	Gem-associated protein 2	protein	201	58% helix, 2% strand	O14893
A	Small nuclear ribonucleoprotein sm D1	protein	80	16% helix, 46% strand	P62314
B	Small nuclear ribonucleoprotein sm D2	protein	95	21% helix, 49% strand	P62316
E	Small nuclear ribonucleoprotein E	protein	75	16% helix, 55% strand	P62304
F	Small nuclear ribonucleoprotein F	protein	74	12% helix, 57% strand	P62306
G	Small nuclear ribonucleoprotein G	protein	58	0% helix, 53% strand	P62308
M	Survival motor neuron protein	protein	17	65% helix, 0% strand	Q16637

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	220	0.60	0.81	27	empty
2	281	0.58	0.77	45	empty
3	260	0.56	0.77	46	empty
4	212	0.53	0.77	34	empty
5	64	0.40	0.79	17	empty

Interfaces

9 interfaces between chains.

2–B · 1054 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 953 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 865 Å² buried · 11 hydrogen bonds · protein-protein
2–M · 854 Å² buried · 8 hydrogen bonds · protein-protein
B–F · 823 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5XJQ · Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with… · the same entry in another collection · chain M against M, TM-score 1.00
O14893 · AlphaFold monomer V2.0 prediction for gem-associated protein 2 (O14893) · a predicted model of the same protein · chain 2 against A, TM-score 0.95
Q16637 · AlphaFold monomer V2.0 prediction for survival motor neuron protein (Q16637) · a predicted model of the same protein · chain M against A, TM-score 0.66

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 O14893
Every structure of UniProt P62314
Every structure of UniProt P62316
Every structure of UniProt P62304
Every structure of UniProt P62306
Every structure of UniProt P62308
Every structure of UniProt Q16637
Elsewhere: RCSB PDB 5XJQ · PDBe 5XJQ · UniProt O14893 · UniProt P62314 · UniProt P62316 · UniProt P62304 · UniProt P62306 · UniProt P62308 · UniProt Q16637

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