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Structure of HIV-1 reverse transcriptase in complex with a 38-mer hairpin template-primer DNA aptamer and an alpha-carboxyphosphonate inhibitor
Analyse Structure of HIV-1 reverse transcriptase in complex with a 38-mer hairpin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HLF
- Type
- protein + DNA
- Length
- 2,003 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
- 64A, GLC, FRU, MG, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase P66 subunit (EC 2.7.7.49) | protein | 554 | 32% helix, 23% strand | P03366 |
| B | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 416 | 37% helix, 19% strand | P03366 |
| C | HIV-1 reverse transcriptase P66 subunit (EC 2.7.7.49) | protein | 553 | 32% helix, 22% strand | P03366 |
| D | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 410 | 36% helix, 21% strand | P03366 |
| E, F | DNA (38-mer) | dna | 35 | — | — |
Ligands and binding sites
- 64A · {[(1S,3R)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}propanedioic acid · ligand · chains A, F
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B, D
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains B, D
- MG · Magnesium ion · metal · 3 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 11 copies · chains A, B, C, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.86 | 0.87 | 91 | GOL |
| 2 | 1028 | 0.86 | 0.87 | 93 | GOL |
| 3 | 1053 | 0.84 | 0.85 | 98 | FRU, GOL |
| 4 | 1143 | 0.82 | 0.83 | 100 | GLC, FRU, GOL |
| 5 | 1082 | 0.78 | 0.79 | 98 | empty |
Interfaces
7 interfaces between chains.
- A–B · 3006 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2926 Ų buried · 37 hydrogen bonds · protein-protein
- A–F · 2096 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–E · 2011 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–C · 394 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5HLF · STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE In COMPLEX WITH A 38-MER HAIRPIN TEMPLATE-PRIMER… · 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 5HLF · PDBe 5HLF · UniProt P03366
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