MolNFT v1 · #38075 · protein
Crystal structure analysis of bacterial 1,5-af reductase
2GLX · 1,5-anhydro-D-fructose reductase: “Crystal structure analysis of bacterial 1,5-af reductase”. X-ray diffraction, 1 ligand (NDP), 15 pockets (best druggability 0.84). MolNFT v1 #38075 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2GLX
- Type
- protein
- Length
- 1,992 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1,5-anhydro-D-fructose reductase
- EC
- 1.1.1.263
- UniProt
- Q2I8V6
- Ligands
- NDP
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 1,5-anhydro-D-fructose reductase (EC 1.1.1.263) | protein | 332 | 38% helix, 25% strand | Q2I8V6 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.84 | 0.85 | 112 | ACT, NDP |
| 2 | 1170 | 0.83 | 0.84 | 119 | ACT, NDP |
| 3 | 457 | 0.71 | 0.82 | 50 | ACT, NDP |
| 4 | 456 | 0.71 | 0.82 | 48 | ACT, NDP |
| 5 | 187 | 0.71 | 0.88 | 30 | empty |
Interfaces
8 interfaces between chains.
- D–F · 1861 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 595 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 560 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 445 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 277 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2GLX · Crystal Structure Analysis of bacterial 1,5-AF Reductase · the same entry in another collection · chain F against F, TM-score 1.00
- Q2I8V6 · AlphaFold monomer V2.0 prediction for 1,5-anhydro-D-fructose reductase (Q2I8V6) · a predicted model of the same protein · chain C 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 Q2I8V6
- Elsewhere: RCSB PDB 2GLX · PDBe 2GLX · UniProt Q2I8V6
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