Research workbench
Crystal structure of malate dehydrogenase from plasmodium falciparum in complex with NADH
Analyse Crystal structure of malate dehydrogenase from plasmodium falciparum in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y91
- Type
- protein
- Length
- 1,205 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- Q6VVP7
- Ligands
- NAD
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate dehydrogenase (EC 1.1.1.37) | protein | 302 | 49% helix, 23% strand | Q6VVP7 |
| B | Malate dehydrogenase (EC 1.1.1.37) | protein | 302 | 51% helix, 23% strand | Q6VVP7 |
| C | Malate dehydrogenase (EC 1.1.1.37) | protein | 300 | 50% helix, 23% strand | Q6VVP7 |
| D | Malate dehydrogenase (EC 1.1.1.37) | protein | 301 | 49% helix, 23% strand | Q6VVP7 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.85 | 0.91 | 74 | empty |
| 2 | 168 | 0.77 | 0.93 | 23 | empty |
| 3 | 178 | 0.76 | 0.92 | 25 | empty |
| 4 | 602 | 0.71 | 0.79 | 76 | NAD |
| 5 | 333 | 0.61 | 0.78 | 38 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1860 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1831 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1448 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1419 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 418 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6Y91 · Crystal structure of malate dehydrogenase from Plasmodium Falciparum in complex with NADH · the same entry in another collection · 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 Q6VVP7
- Elsewhere: RCSB PDB 6Y91 · PDBe 6Y91 · UniProt Q6VVP7
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