MolNFT v1 · #38080 · protein

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

2GM3 · Unknown protein: “Crystal structure of an universal stress protein family protein from arabidopsis thaliana AT3G01520 with AMP…”. X-ray diffraction, 1 ligand (AMP), 11 pockets (best druggability 0.72). MolNFT v1 #38080 on GenesisL1…

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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