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Structure of RGLG1 mutant-D207G

Analyse Structure of RGLG1 mutant-D207G in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6K83
Type: protein
Length: 2,240 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase RGLG1
EC: 2.3.2.27
UniProt: Q9SS90
Ligands: CA, MG
Pockets: 20 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A, C, D, E, F, G, H	E3 ubiquitin-protein ligase RGLG1 (EC 2.3.2.27)	protein	280	39% helix, 15% strand	Q9SS90

Ligands and binding sites

CA · Calcium ion · metal · 24 copies · chains B, A, C, D, E, F, G, H
MG · Magnesium ion · metal · 8 copies · chains B, C, A, D, E, G, F, H

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

Pockets

20 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	525	0.63	0.76	57	CA
2	200	0.53	0.78	33	empty
3	140	0.50	0.79	22	empty
4	120	0.50	0.80	20	empty
5	141	0.49	0.79	22	empty

Interfaces

10 interfaces between chains.

C–D · 914 Å² buried · 20 hydrogen bonds · protein-protein
B–A · 895 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 888 Å² buried · 17 hydrogen bonds · protein-protein
E–H · 866 Å² buried · 16 hydrogen bonds · protein-protein
E–G · 836 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6K83 · Structure of RGLG1 mutant-D207G · the same entry in another collection · chain H against H, TM-score 1.00
Q9SS90 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RGLG1 (Q9SS90) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q9SS90
Elsewhere: RCSB PDB 6K83 · PDBe 6K83 · UniProt Q9SS90

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