Research workbench
Crystal structure of malate dehydrogenase from trypanosoma cruzi
Analyse Crystal structure of malate dehydrogenase from trypanosoma cruzi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NRZ
- Type
- protein
- Length
- 2,584 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- EC
- 1.1.1.37
- UniProt
- Q4DRD8
- Ligands
- CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Malate dehydrogenase (EC 1.1.1.37) | protein | 323 | 47% helix, 17% strand | Q4DRD8 |
Ligands and binding sites
- CL · Chloride ion · ion · chains G
- EDO · 1,2-ethanediol · additive · 79 copies · chains A, B, C, D, H, E, G, F
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, C, E, F
- PGE · Triethylene glycol · additive · 2 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · 2 copies · chains C, D, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.78 | 0.82 | 80 | EDO, PGE, PEG, PG4 |
| 2 | 704 | 0.77 | 0.82 | 82 | EDO |
| 3 | 739 | 0.77 | 0.81 | 84 | PGE, EDO |
| 4 | 678 | 0.76 | 0.82 | 81 | EDO |
| 5 | 772 | 0.74 | 0.79 | 93 | EDO |
Interfaces
14 interfaces between chains.
- A–B · 1895 Ų buried · 39 hydrogen bonds · protein-protein
- G–H · 1867 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 1858 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 1828 Ų buried · 39 hydrogen bonds · protein-protein
- F–H · 635 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7NRZ · Crystal structure of malate dehydrogenase from Trypanosoma cruzi · 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 Q4DRD8
- Elsewhere: RCSB PDB 7NRZ · PDBe 7NRZ · UniProt Q4DRD8
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