Research workbench
Crystal structure of saccharomyces cerevisiae arabinose dehydrogenase ARA1 complexed with NADPH
Analyse Crystal structure of saccharomyces cerevisiae arabinose dehydrogenase ARA1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IJR
- Type
- protein
- Length
- 656 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-arabinose dehydrogenase [NAD(P)+] heavy chain
- EC
- 1.1.1.117
- UniProt
- P38115
- Ligands
- NDP
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | D-arabinose dehydrogenase [NAD(P)+] heavy chain (EC 1.1.1.117) | protein | 328 | 41% helix, 17% strand | P38115 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.71 | 0.82 | 51 | NDP |
| 2 | 408 | 0.70 | 0.82 | 49 | NDP |
| 3 | 429 | 0.63 | 0.77 | 39 | empty |
| 4 | 386 | 0.60 | 0.76 | 45 | empty |
| 5 | 359 | 0.58 | 0.76 | 43 | empty |
Interfaces
1 interface between chains.
- A–C · 995 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4IJR · Crystal structure of Saccharomyces cerevisiae arabinose dehydrogenase Ara1 complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P38115 · AlphaFold monomer V2.0 prediction for D-arabinose dehydrogenase [NAD(P)+] heavy chain… · a predicted model of the same protein · chain A 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 P38115
- Elsewhere: RCSB PDB 4IJR · PDBe 4IJR · UniProt P38115
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