Research workbench
Stabilization of a tetrameric malate dehydrogenase by introduction of a disulfide bridge at the DIMER/DIMER interface
Analyse Stabilization of a tetrameric malate dehydrogenase by introduction of a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UR5
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- P80040
- Ligands
- NAD, CD, NA, CL
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate dehydrogenase (EC 1.1.1.37) | protein | 298 | 51% helix, 21% strand | P80040 |
| C | Malate dehydrogenase (EC 1.1.1.37) | protein | 300 | 52% helix, 21% strand | P80040 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, C
- CD · Cadmium ion · metal · 6 copies · chains A, C
- NA · Sodium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.62 | 0.79 | 47 | NAD, CD |
| 2 | 411 | 0.60 | 0.75 | 66 | empty |
| 3 | 360 | 0.60 | 0.77 | 47 | NAD, CD, CL |
Interfaces
1 interface between chains.
- A–C · 1186 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1UR5 · Stabilization of a Tetrameric Malate Dehydrogenase by Introduction of a Disulfide Bridge… · the same entry in another collection · chain A against A, TM-score 1.00
- P80040 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (P80040) · a predicted model of the same protein · chain A 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 P80040
- Elsewhere: RCSB PDB 1UR5 · PDBe 1UR5 · UniProt P80040
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