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Crystal structure of an universal stress protein family protein from arabidopsis thaliana AT3G01520 with AMP bound

Analyse Crystal structure of an universal stress protein family protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GM3
Type: protein
Length: 905 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Unknown protein
UniProt: Q8LGG8
Ligands: AMP
Pockets: 11 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, E	Unknown protein	protein	153	42% helix, 24% strand	Q8LGG8
B	Unknown protein	protein	145	40% helix, 25% strand	Q8LGG8
F	Unknown protein	protein	148	41% helix, 24% strand	Q8LGG8

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

11 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	498	0.72	0.81	67	AMP
2	549	0.71	0.80	79	AMP
3	601	0.71	0.79	86	AMP
4	282	0.52	0.74	34	empty
5	176	0.46	0.76	21	empty

Interfaces

7 interfaces between chains.

A–B · 1073 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 1064 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 1053 Å² buried · 25 hydrogen bonds · protein-protein
C–E · 871 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 182 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 modified (engineered).

Compared structures

2GM3 · Crystal Structure of an Universal Stress Protein Family Protein from Arabidopsis Thaliana… · the same entry in another collection · chain F against F, TM-score 1.00
Q8LGG8 · AlphaFold monomer V2.0 prediction for universal stress protein a-like protein (Q8LGG8) · a predicted model of the same protein · chain A against A, TM-score 0.90

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 Q8LGG8
Elsewhere: RCSB PDB 2GM3 · PDBe 2GM3 · UniProt Q8LGG8

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