Research workbench
Crystal structure of plasmodium vivax ldh in complex with a DNA aptamer called PL1 (tetrameric ldh in an asymmetric unit)
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
- 5HTO
- Type
- protein + DNA
- Length
- 1,278 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase; DNA (34-mer); DNA (30-mer)
- EC
- 1.1.1.27
- UniProt
- Q4PRK9
- Ligands
- MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 302 | 49% helix, 21% strand | Q4PRK9 |
| B | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 303 | 50% helix, 21% strand | Q4PRK9 |
| C | DNA (34-mer) | dna | 34 | — | — |
| D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 304 | 49% helix, 21% strand | Q4PRK9 |
| E | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 305 | 50% helix, 21% strand | Q4PRK9 |
| F | DNA (30-mer) | dna | 30 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.84 | 0.87 | 95 | empty |
| 2 | 1024 | 0.84 | 0.84 | 67 | empty |
| 3 | 1157 | 0.83 | 0.84 | 106 | empty |
| 4 | 191 | 0.82 | 0.97 | 48 | empty |
| 5 | 187 | 0.81 | 0.96 | 44 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2199 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 2197 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 1275 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1269 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 592 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 5HTO · 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 5HTO · PDBe 5HTO · UniProt Q4PRK9
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