Research workbench
Crystal structure of the lactate dehydrogenase from cryptosporidium parvum
Analyse Crystal structure of the lactate dehydrogenase from cryptosporidium parvum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ND5
- Type
- protein
- Length
- 1,201 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- Q5CYZ2
- Pockets
- 16 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase (EC 1.1.1.27) | protein | 302 | 50% helix, 23% strand | Q5CYZ2 |
| B | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase (EC 1.1.1.27) | protein | 301 | 50% helix, 21% strand | Q5CYZ2 |
| C | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase (EC 1.1.1.27) | protein | 300 | 51% helix, 20% strand | Q5CYZ2 |
| D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase (EC 1.1.1.27) | protein | 298 | 51% helix, 20% strand | Q5CYZ2 |
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.64 | 0.82 | 40 | empty |
| 2 | 350 | 0.62 | 0.78 | 51 | empty |
| 3 | 181 | 0.54 | 0.79 | 24 | empty |
| 4 | 134 | 0.52 | 0.81 | 36 | empty |
| 5 | 154 | 0.52 | 0.79 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2077 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2026 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 426 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4ND5 · Crystal structure of the lactate dehydrogenase from cryptosporidium parvum · 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 Q5CYZ2
- Elsewhere: RCSB PDB 4ND5 · PDBe 4ND5 · UniProt Q5CYZ2
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