Research workbench
Crystal structure of malate dehydrogenase from plasmodium falciparum (pfmdh)
Analyse Crystal structure of malate dehydrogenase from plasmodium falciparum (pfmdh) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NFR
- Type
- protein
- Length
- 5,004 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- C6KT25
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H, I, J, K, L, M, N, O, P | Malate dehydrogenase (EC 1.1.1.37) | protein | 313 | 49% helix, 23% strand | C6KT25 |
| G | Malate dehydrogenase (EC 1.1.1.37) | protein | 309 | 50% helix, 23% strand | C6KT25 |
Ligands and binding sites
- CIT · Citric acid · additive · 15 copies · chains A, B, C, D, E, F, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.88 | 0.89 | 118 | empty |
| 2 | 1174 | 0.88 | 0.89 | 123 | empty |
| 3 | 1154 | 0.88 | 0.89 | 121 | empty |
| 4 | 366 | 0.83 | 0.92 | 51 | empty |
| 5 | 355 | 0.82 | 0.92 | 53 | empty |
Interfaces
32 interfaces between chains.
- A–B · 1913 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1912 Ų buried · 23 hydrogen bonds · protein-protein
- K–L · 1911 Ų buried · 22 hydrogen bonds · protein-protein
- I–J · 1904 Ų buried · 23 hydrogen bonds · protein-protein
- M–N · 1893 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5NFR · Crystal structure of malate dehydrogenase from Plasmodium falciparum (PfMDH) · 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 C6KT25
- Elsewhere: RCSB PDB 5NFR · PDBe 5NFR · UniProt C6KT25
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