MolNFT v1 · #165509 · protein
Structural insights into cubane-modified aptamer recognition of a malaria biomarker
6TXR · L-lactate dehydrogenase: “Structural insights into cubane-modified aptamer recognition of a malaria biomarker”. X-ray diffraction, 5 ligands (DG, DC, DA), 17 pockets (best druggability 0.82). MolNFT v1 #165509 on GenesisL1: 3D…
- PDB
- 6TXR
- Type
- protein
- Length
- 1,222 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-lactate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- Q4PRK9
- Ligands
- DG, DC, DA, DU, O0Q
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 306 | 49% helix, 21% strand | Q4PRK9 |
| B, C | L-lactate dehydrogenase (EC 1.1.1.27) | protein | 305 | 49% helix, 21% strand | Q4PRK9 |
Ligands and binding sites
- DG · 2'-deoxyguanosine-5'-monophosphate · ligand · 22 copies · chains A, B, D
- DC · 2'-deoxycytidine-5'-monophosphate · ligand · 20 copies · chains A, B, C, D
- DA · 2'-deoxyadenosine-5'-monophosphate · ligand · 16 copies · chains B, D
- DU · 2'-deoxyuridine-5'-monophosphate · ligand · 10 copies · chains B, A, D, C
- O0Q · ~{N}-[2-(1,2,3-triazol-1-yl)ethyl]cubane-1-carboxamide · ligand · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.82 | 0.95 | 47 | empty |
| 2 | 224 | 0.82 | 0.95 | 45 | empty |
| 3 | 1177 | 0.81 | 0.82 | 61 | empty |
| 4 | 619 | 0.70 | 0.78 | 57 | empty |
| 5 | 597 | 0.70 | 0.78 | 54 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2192 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2192 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1324 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1291 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 499 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6TXR · Structural insights into cubane-modified aptamer recognition of a malaria biomarker · 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 6TXR · PDBe 6TXR · UniProt Q4PRK9
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