MolNFT v1 · #34415 · protein
Crystal structure of human malate dehydrogenase type 2
2DFD: “Crystal structure of human malate dehydrogenase type 2”. X-ray diffraction, 4 ligands (MLT, NAD, HIS), 9 pockets (best druggability 0.80). MolNFT v1 #34415 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2DFD
- Type
- protein
- Length
- 1,258 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- P40926
- Ligands
- MLT, NAD, HIS, CL
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate dehydrogenase (EC 1.1.1.37) | protein | 316 | 47% helix, 19% strand | P40926 |
| B, C, D | Malate dehydrogenase (EC 1.1.1.37) | protein | 314 | 49% helix, 19% strand | P40926 |
Ligands and binding sites
- MLT · D-malate · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- HIS · Histidine · ligand · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.80 | 0.82 | 116 | MLT, NAD |
| 2 | 631 | 0.75 | 0.81 | 93 | MLT, NAD |
| 3 | 312 | 0.70 | 0.84 | 50 | MLT, NAD |
| 4 | 221 | 0.48 | 0.74 | 22 | empty |
| 5 | 168 | 0.40 | 0.72 | 22 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1563 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1553 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 449 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 423 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2DFD · Crystal Structure of Human Malate Dehydrogenase Type 2 · the same entry in another collection · chain D against D, TM-score 1.00
- P40926 · AlphaFold monomer V2.0 prediction for malate dehydrogenase, mitochondrial (P40926) · a predicted model of the same protein · chain B 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 P40926
- Elsewhere: RCSB PDB 2DFD · PDBe 2DFD · UniProt P40926
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