Research workbench
Structure of plasmodium falciparum lactate dehydrogenase in complex with a DNA aptamer
Analyse Structure of plasmodium falciparum lactate dehydrogenase in complex with a DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZH2
- Type
- protein + DNA
- Length
- 1,302 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase; DNA aptamer
- EC
- 1.1.1.27
- UniProt
- Q76NM3
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 314 | 48% helix, 20% strand | Q76NM3 |
| B | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 308 | 49% helix, 20% strand | Q76NM3 |
| C | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 315 | 49% helix, 20% strand | Q76NM3 |
| D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 311 | 49% helix, 20% strand | Q76NM3 |
| E, G | DNA aptamer | dna | 27 | — | — |
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.83 | 0.84 | 81 | empty |
| 2 | 208 | 0.83 | 0.96 | 45 | empty |
| 3 | 203 | 0.83 | 0.97 | 46 | empty |
| 4 | 1122 | 0.80 | 0.82 | 121 | empty |
| 5 | 611 | 0.74 | 0.81 | 60 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2199 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2191 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1268 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1232 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 908 Ų buried · 26 hydrogen bonds · protein-nucleic
Compared structures
- 3ZH2 · Structure of Plasmodium falciparum lactate dehydrogenase in complex with a DNA aptamer · 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 Q76NM3
- Elsewhere: RCSB PDB 3ZH2 · PDBe 3ZH2 · UniProt Q76NM3
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