MolNFT v1 · #48486 · protein
The crystal structure of isomerase domain of glucosamine-6-phosphate synthase from candida albicans
2PUV · Isomerase domain of glutamine-fructose-6-phosphate…: “The crystal structure of isomerase domain of glucosamine-6-phosphate synthase from candida albicans”. X-ray diffraction, 3 ligands (UD1, M6R, NA), 11 pockets (best druggability…
- PDB
- 2PUV
- Type
- protein
- Length
- 1,378 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing)
- EC
- 2.6.1.16
- UniProt
- P53704
- Ligands
- UD1, M6R, NA
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing) (EC 2.6.1.16) | protein | 338 | 51% helix, 17% strand | P53704 |
| B | Isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing) (EC 2.6.1.16) | protein | 352 | 50% helix, 17% strand | P53704 |
| C | Isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing) (EC 2.6.1.16) | protein | 348 | 49% helix, 17% strand | P53704 |
| D | Isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing) (EC 2.6.1.16) | protein | 340 | 50% helix, 17% strand | P53704 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 4 copies · chains A, B, C, D
- M6R · 5-amino-5-deoxy-1-O-phosphono-D-mannitol · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.87 | 0.88 | 67 | empty |
| 2 | 1176 | 0.84 | 0.85 | 101 | ACT, M6R |
| 3 | 1180 | 0.84 | 0.85 | 95 | ACT |
| 4 | 270 | 0.55 | 0.77 | 34 | M6R |
| 5 | 228 | 0.52 | 0.77 | 29 | M6R |
Interfaces
6 interfaces between chains.
- A–B · 1719 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1662 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 570 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 559 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 376 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2PUV · The crystal structure of isomerase domain of glucosamine-6-phosphate synthase from… · the same entry in another collection · chain D against D, TM-score 1.00
- P53704 · AlphaFold monomer V2.0 prediction for glutamine--fructose-6-phosphate aminotransferase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P53704
- Elsewhere: RCSB PDB 2PUV · PDBe 2PUV · UniProt P53704
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