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Crystal structure of human gfat-1 L405R

Analyse Crystal structure of human gfat-1 L405R in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZMK
Type: protein
Length: 1,312 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
EC: 2.6.1.16
UniProt: Q06210
Ligands: G6Q, GLU
Pockets: 13 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (EC 2.6.1.16)	protein	656	38% helix, 25% strand	Q06210
B	Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (EC 2.6.1.16)	protein	656	38% helix, 23% strand	Q06210

Ligands and binding sites

G6Q · Glucose-6-phosphate · ligand · 2 copies · chains A, B
GLU · Glutamic acid · ligand · chains A

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	617	0.87	0.91	58	empty
2	1021	0.80	0.82	122	empty
3	986	0.80	0.81	83	G6Q, GLU
4	109	0.78	0.98	27	G6Q
5	127	0.50	0.80	12	empty

Interfaces

1 interface between chains.

A–B · 2904 Å² buried · 52 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

6ZMK · Crystal structure of human GFAT-1 L405R · the same entry in another collection · chain A against A, TM-score 1.00
Q06210 · AlphaFold monomer V2.0 prediction for glutamine--fructose-6-phosphate aminotransferase… · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q06210
Elsewhere: RCSB PDB 6ZMK · PDBe 6ZMK · UniProt Q06210

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