Research workbench
Structure and catalytic mechanism of monodehydroascorbate reductase, mdhar, from oryza sativa L. japonica
Analyse Structure and catalytic mechanism of monodehydroascorbate reductase, mdhar… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JCL
- Type
- protein
- Length
- 857 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- OS09G0567300 protein
- UniProt
- Q652L6
- Ligands
- FAD, NDP
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | OS09G0567300 protein | protein | 429 | 28% helix, 31% strand | Q652L6 |
| B | OS09G0567300 protein | protein | 428 | 27% helix, 32% strand | Q652L6 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.86 | 0.89 | 107 | NDP, FAD |
| 2 | 793 | 0.82 | 0.84 | 85 | FAD, NDP |
| 3 | 140 | 0.65 | 0.87 | 30 | empty |
| 4 | 67 | 0.44 | 0.81 | 13 | empty |
| 5 | 83 | 0.43 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 770 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5JCL · Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza… · the same entry in another collection · chain A against A, TM-score 1.00
- Q652L6 · AlphaFold monomer V2.0 prediction for monodehydroascorbate reductase 3, cytosolic (Q652L6) · a predicted model of the same protein · chain B 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 Q652L6
- Elsewhere: RCSB PDB 5JCL · PDBe 5JCL · UniProt Q652L6
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