MolNFT v1 · #153726 · protein
Crystal structure of azospirillum brasilense L-arabinose 1- dehydrogenase (apo-form)
6JNJ · L-arabinose 1-dehydrogenase (NAD(P)(+)): “Crystal structure of azospirillum brasilense L-arabinose 1- dehydrogenase (apo-form)”. X-ray diffraction, 1 ligand (PO4), 5 pockets (best druggability 0.67). MolNFT v1 #153726 on GenesisL1…
- PDB
- 6JNJ
- Type
- protein
- Length
- 613 residues
- Chains
- 2
- 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
- PO4
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 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 |
| B | L-arabinose 1-dehydrogenase (NAD(P)(+)) (EC 1.1.1.376, 1.1.1.120, 1.1.1.48) | protein | 307 | 36% helix, 29% strand | Q53TZ2 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.67 | 0.78 | 45 | PO4 |
| 2 | 527 | 0.67 | 0.78 | 45 | PO4 |
| 3 | 159 | 0.54 | 0.81 | 16 | empty |
| 4 | 114 | 0.40 | 0.75 | 18 | empty |
| 5 | 80 | 0.34 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1546 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6JNJ · Crystal structure of Azospirillum brasilense L-arabinose 1-dehydrogenase (apo-form) · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.97
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 6JNJ · PDBe 6JNJ · UniProt Q53TZ2
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