Research workbench
Crystal structure of cryptosporidium parvum malate dehydrogenase
Analyse Crystal structure of cryptosporidium parvum malate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HJR
- Type
- protein
- Length
- 3,763 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate dehydrogenase
- UniProt
- Q5CYZ3
- Ligands
- APR
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G, I, K | Malate dehydrogenase | protein | 313 | 50% helix, 20% strand | Q5CYZ3 |
| B, C, D, F, H, J, L | Malate dehydrogenase | protein | 314 | 50% helix, 20% strand | Q5CYZ3 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CIT · Citric acid · additive · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 787 | 0.83 | 0.86 | 89 | empty |
| 2 | 818 | 0.83 | 0.86 | 99 | empty |
| 3 | 855 | 0.83 | 0.85 | 89 | empty |
| 4 | 741 | 0.82 | 0.85 | 85 | empty |
| 5 | 649 | 0.81 | 0.85 | 64 | empty |
Interfaces
22 interfaces between chains.
- B–C · 1991 Ų buried · 23 hydrogen bonds · protein-protein
- E–G · 1981 Ų buried · 24 hydrogen bonds · protein-protein
- I–L · 1975 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1958 Ų buried · 26 hydrogen bonds · protein-protein
- J–K · 1950 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2HJR · Crystal Structure of Cryptosporidium parvum malate dehydrogenase · 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 Q5CYZ3
- Elsewhere: RCSB PDB 2HJR · PDBe 2HJR · UniProt Q5CYZ3
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