Research workbench
Structure of HIV-1 reverse transcriptase in complex with a DNA aptamer and foscarnet, a pyrophosphate analog
Analyse Structure of HIV-1 reverse transcriptase in complex with a DNA aptamer and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HP1
- Type
- protein + DNA
- Length
- 2,002 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase P66 subunit; HIV-1 reverse transcriptase P51 subunit; DNA…
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- PPF, ATM, GLC, FRU, MG, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HIV-1 reverse transcriptase P66 subunit (EC 2.7.7.49) | protein | 553 | 33% helix, 24% strand | P03366 |
| B | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 416 | 36% helix, 20% strand | P03366 |
| F, E | DNA (38-mer) | dna | 35 | — | — |
| D | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 410 | 37% helix, 21% strand | P03366 |
Ligands and binding sites
- PPF · Phosphonoformic acid · ligand · 2 copies · chains A, C
- ATM · 3'-azido-3'-deoxythymidine-5'-monophosphate · ligand · 2 copies · chains A, F, C, E
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B, D
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains B, D
- MG · Magnesium ion · metal · 8 copies · chains A, F, C, E
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.86 | 0.87 | 88 | empty |
| 2 | 1031 | 0.86 | 0.87 | 91 | empty |
| 3 | 1027 | 0.84 | 0.85 | 92 | GOL |
| 4 | 1060 | 0.83 | 0.84 | 96 | empty |
| 5 | 1096 | 0.77 | 0.79 | 96 | empty |
Interfaces
7 interfaces between chains.
- A–B · 3006 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2958 Ų buried · 36 hydrogen bonds · protein-protein
- A–F · 2083 Ų buried · 22 hydrogen bonds · protein-nucleic
- C–E · 2018 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 392 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent (nucleotide modification, covalent ligand).
Compared structures
- 5HP1 · STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE In COMPLEX WITH A DNA aptamer and FOSCARNET, a… · 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 P03366
- Elsewhere: RCSB PDB 5HP1 · PDBe 5HP1 · UniProt P03366
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