MolNFT v1 · #34042 · protein

Crystal structure of the maize glutamine synthetase complexed with ADP and phosphinothricin phosphate

2D3C: “Crystal structure of the maize glutamine synthetase complexed with ADP and phosphinothricin phosphate”. X-ray diffraction, 3 ligands (P3P, ADP, MN), 20 pockets (best druggability 0.75). MolNFT v1 #34042 on GenesisL1: 3D structure…

PDB: 2D3C
Type: protein
Length: 3,530 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamine synthetase
EC: 6.3.1.2
UniProt: P38561
Ligands: P3P, ADP, MN
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Glutamine synthetase (EC 6.3.1.2)	protein	353	30% helix, 25% strand	P38561

Ligands and binding sites

P3P · (2S)-2-amino-4-[methyl(phosphonooxy)phosphoryl]butanoic acid · ligand · 10 copies · chains A, B, C, E, D, F, G, H, J, I
ADP · Adenosine-5'-diphosphate · ligand · 10 copies · chains A, B, C, E, D, F, G, H, J, I
MN · Manganese (II) ion · metal · 30 copies · chains A, B, C, D, E, F, G, H, I, J

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	499	0.75	0.84	64	MN, P3P, ADP
2	525	0.75	0.83	64	MN, P3P, ADP
3	565	0.75	0.83	65	MN, P3P, ADP
4	546	0.75	0.83	62	MN, P3P, ADP
5	550	0.75	0.83	69	MN, P3P, ADP

Interfaces

20 interfaces between chains.

C–E · 2021 Å² buried · 38 hydrogen bonds · protein-protein
I–J · 2013 Å² buried · 38 hydrogen bonds · protein-protein
F–G · 2013 Å² buried · 39 hydrogen bonds · protein-protein
A–D · 2009 Å² buried · 39 hydrogen bonds · protein-protein
B–C · 2008 Å² buried · 40 hydrogen bonds · protein-protein

Compared structures

2D3C · Crystal Structure of the Maize Glutamine Synthetase complexed with ADP and… · the same entry in another collection · chain J against J, TM-score 1.00
P38561 · AlphaFold monomer V2.0 prediction for glutamine synthetase root isozyme 3 (P38561) · 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 P38561
Elsewhere: RCSB PDB 2D3C · PDBe 2D3C · UniProt P38561

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.