Research workbench
Crystal structure of plasmodium vivax ldh in complex with a DNA aptamer called PL1
Analyse Crystal structure of plasmodium vivax ldh in complex with a DNA aptamer called… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HRU
- Type
- protein + DNA
- Length
- 643 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase; DNA (32-mer)
- EC
- 1.1.1.27
- UniProt
- Q4PRK9
- Ligands
- MG
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 305 | 49% helix, 21% strand | Q4PRK9 |
| B | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 306 | 50% helix, 21% strand | Q4PRK9 |
| C | DNA (32-mer) | dna | 32 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.85 | 0.86 | 99 | empty |
| 2 | 443 | 0.74 | 0.83 | 51 | empty |
| 3 | 95 | 0.42 | 0.78 | 20 | empty |
| 4 | 60 | 0.38 | 0.80 | 17 | empty |
| 5 | 93 | 0.33 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2193 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 627 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 528 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 5HRU · Crystal structure of Plasmodium vivax LDH in complex with a DNA aptamer called pL1 · 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 Q4PRK9
- Elsewhere: RCSB PDB 5HRU · PDBe 5HRU · UniProt Q4PRK9
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