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Crystal structure of the GEMIN2-binding domain of smn, GEMIN2DN39 in complex with SMD1(1-82)/D2/F/E from human

Analyse Crystal structure of the GEMIN2-binding domain of smn, GEMIN2DN39 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XJS
Type: protein
Length: 542 residues
Chains: 6
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, Q16637
Pockets: 9 · best druggability 0.58

Structure

x-ray diffraction · 6 distinct chains · 33% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	Gem-associated protein 2	protein	201	57% helix, 2% strand	O14893
A	Small nuclear ribonucleoprotein sm D1	protein	80	15% helix, 46% strand	P62314
B	Small nuclear ribonucleoprotein sm D2	protein	95	21% helix, 48% strand	P62316
E	Small nuclear ribonucleoprotein E	protein	75	17% helix, 55% strand	P62304
F	Small nuclear ribonucleoprotein F	protein	74	12% helix, 57% strand	P62306
M	Survival motor neuron protein	protein	17	65% helix, 0% strand	Q16637

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	191	0.58	0.81	26	empty
2	167	0.53	0.79	33	empty
3	164	0.50	0.78	32	empty
4	132	0.44	0.76	21	empty
5	85	0.33	0.73	18	empty

Interfaces

8 interfaces between chains.

2–B · 1065 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 968 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 884 Å² buried · 15 hydrogen bonds · protein-protein
2–M · 875 Å² buried · 9 hydrogen bonds · protein-protein
B–F · 853 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5XJS · Crystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39 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 0.94
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 0.68

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 Q16637
Elsewhere: RCSB PDB 5XJS · PDBe 5XJS · UniProt O14893 · UniProt P62314 · UniProt P62316 · UniProt P62304 · UniProt P62306 · UniProt Q16637

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