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The structure of the GEMIN5 WD40 domain with aauuuuug

Analyse The structure of the GEMIN5 WD40 domain with aauuuuug in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GXH
Type: protein + RNA
Length: 678 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gem-associated protein 5; RNA (5'-R(*A*AP*UP*UP*UP*UP*UP*G)-3')
UniProt: Q8TEQ6
Ligands: UNX
Pockets: 7 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gem-associated protein 5	protein	672	4% helix, 47% strand	Q8TEQ6
B	RNA (5'-R(AAPUPUPUPUPUPG)-3')	rna	6	—	—

Ligands and binding sites

UNX · Unknown atom or ion · ion · 3 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

7 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	834	0.79	0.82	58	UNX
2	518	0.76	0.83	51	GOL
3	155	0.47	0.77	30	empty
4	152	0.47	0.77	23	GOL, UNX
5	87	0.39	0.77	22	empty

Interfaces

1 interface between chains.

A–B · 885 Å² buried · 18 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5GXH · The structure of the Gemin5 WD40 domain with AAUUUUUG · the same entry in another collection · chain A against A, TM-score 1.00
Q8TEQ6 · AlphaFold monomer V2.0 prediction for gem-associated protein 5 (Q8TEQ6) · a predicted model of the same protein · 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 Q8TEQ6
Elsewhere: RCSB PDB 5GXH · PDBe 5GXH · UniProt Q8TEQ6

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