Research workbench
The isomerase domain of human glutamine-fructose-6-phosphate transaminase 1 (GFPT1) in complex with fructose 6-phosphate
Analyse The isomerase domain of human glutamine-fructose-6-phosphate transaminase 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V4M
- Type
- protein
- Length
- 1,405 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1
- EC
- 2.6.1.16
- UniProt
- Q06210
- Ligands
- F6R, CL
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (EC 2.6.1.16) | protein | 352 | 51% helix, 17% strand | Q06210 |
| B | Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (EC 2.6.1.16) | protein | 351 | 51% helix, 17% strand | Q06210 |
| C | Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (EC 2.6.1.16) | protein | 352 | 52% helix, 17% strand | Q06210 |
| D | Glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (EC 2.6.1.16) | protein | 350 | 52% helix, 17% strand | Q06210 |
Ligands and binding sites
- F6R · Fructose -6-phosphate · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.87 | 0.92 | 59 | empty |
| 2 | 626 | 0.87 | 0.91 | 62 | empty |
| 3 | 379 | 0.85 | 0.94 | 38 | empty |
| 4 | 669 | 0.76 | 0.82 | 65 | empty |
| 5 | 692 | 0.73 | 0.79 | 71 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2237 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2158 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 538 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 533 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 403 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2V4M · The isomerase domain of human glutamine-fructose-6-phosphate transaminase 1 (GFPT1) in… · the same entry in another collection · chain D against D, TM-score 1.00
- Q06210 · AlphaFold monomer V2.0 prediction for glutamine--fructose-6-phosphate aminotransferase… · a predicted model of the same protein · chain D 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 Q06210
- Elsewhere: RCSB PDB 2V4M · PDBe 2V4M · UniProt Q06210
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