Research workbench
Crystal structure of NAD(H)-depenent malate dehydrogenase complexed with NADPH
Analyse Crystal structure of NAD(H)-depenent malate dehydrogenase complexed with NADPH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y7T
- Type
- protein
- Length
- 654 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- P10584
- Ligands
- NDP
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Malate dehydrogenase (EC 1.1.1.37) | protein | 327 | 46% helix, 19% strand | P10584 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.63 | 0.77 | 48 | NDP, TRS |
| 2 | 414 | 0.61 | 0.76 | 45 | NDP, TRS |
| 3 | 237 | 0.53 | 0.77 | 38 | empty |
| 4 | 201 | 0.50 | 0.77 | 36 | empty |
| 5 | 113 | 0.46 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1655 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 1Y7T · Crystal structure of NAD(H)-depenent malate dehydrogenase complexed with NADPH · the same entry in another collection · chain A against A, TM-score 1.00
- P10584 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (P10584) · 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 P10584
- Elsewhere: RCSB PDB 1Y7T · PDBe 1Y7T · UniProt P10584
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