MolNFT v1 · #153727 · protein
Crystal structure of azospirillum brasilense L-arabinose 1- dehydrogenase (NADP-bound form)
6JNK · L-arabinose 1-dehydrogenase (NAD(P)(+)): “Crystal structure of azospirillum brasilense L-arabinose 1- dehydrogenase (NADP-bound form)”. X-ray diffraction, 1 ligand (NAP), 13 pockets (best druggability 0.80). MolNFT v1 #153727 on…
- PDB
- 6JNK
- Type
- protein
- Length
- 1,224 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-arabinose 1-dehydrogenase (NAD(P)(+))
- EC
- 1.1.1.376, 1.1.1.120, 1.1.1.48
- UniProt
- Q53TZ2
- Ligands
- NAP
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-arabinose 1-dehydrogenase (NAD(P)(+)) (EC 1.1.1.376, 1.1.1.120, 1.1.1.48) | protein | 306 | 36% helix, 29% strand | Q53TZ2 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.80 | 0.82 | 112 | NAP |
| 2 | 514 | 0.70 | 0.80 | 50 | NAP |
| 3 | 512 | 0.68 | 0.79 | 48 | NAP |
| 4 | 541 | 0.68 | 0.78 | 46 | NAP |
| 5 | 147 | 0.60 | 0.84 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1393 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1345 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 514 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 64 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6JNK · Crystal structure of Azospirillum brasilense L-arabinose 1-dehydrogenase (NADP-bound form) · the same entry in another collection · chain C against C, TM-score 1.00
- Q53TZ2 · AlphaFold monomer V2.0 prediction for L-arabinose 1-dehydrogenase (NAD(P)(+)) (Q53TZ2) · a predicted model of the same protein · chain B 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 Q53TZ2
- Elsewhere: RCSB PDB 6JNK · PDBe 6JNK · UniProt Q53TZ2
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