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Crystal structure of human gfat-1 in complex with glucose-6-phosphate, L-glu, and udp-galnac
Analyse Crystal structure of human gfat-1 in complex with glucose-6-phosphate, L-glu… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SVM
- Type
- protein
- Length
- 1,315 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, UD2, GLU, MG
- Pockets
- 13 · best druggability 0.86
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 | 660 | 39% helix, 25% strand | Q06210 |
| B | Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (EC 2.6.1.16) | protein | 655 | 38% helix, 23% strand | Q06210 |
Ligands and binding sites
- G6Q · Glucose-6-phosphate · ligand · 2 copies · chains A, B
- UD2 · Uridine-diphosphate-N-acetylgalactosamine · ligand · 2 copies · chains A, B
- GLU · Glutamic acid · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.86 | 0.91 | 57 | empty |
| 2 | 950 | 0.79 | 0.81 | 94 | empty |
| 3 | 1182 | 0.79 | 0.81 | 99 | G6Q, GLU |
| 4 | 119 | 0.78 | 0.97 | 25 | G6Q |
| 5 | 123 | 0.49 | 0.79 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2917 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 6SVM · Crystal structure of human GFAT-1 in complex with Glucose-6-Phosphate, L-Glu, and… · 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 6SVM · PDBe 6SVM · UniProt Q06210
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