MolNFT v1 · #121313 · protein + DNA
Structure of HIV-1 reverse transcriptase in complex with a DNA aptamer and an alpha-carboxy nucleoside phosphonate inhibitor (alpha-cnp)
5HRO · HIV-1 reverse transcriptase P66 subunit: “Structure of HIV-1 reverse transcriptase in complex with a DNA aptamer and an alpha-carboxy nucleoside…”. X-ray diffraction, 5 ligands (3JY, GLC, FRU), 20 pockets (best druggability 0.85).…
- PDB
- 5HRO
- Type
- protein + DNA
- Length
- 1,996 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
- 3JY, GLC, FRU, MG, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 33% 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 | 551 | 32% helix, 23% strand | P03366 |
| B, D | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 412 | 35% helix, 20% strand | P03366 |
| E, F | DNA (38-mer) | dna | 35 | — | — |
Ligands and binding sites
- 3JY · [(1R)-2-methoxy-1-{[(1S,3R)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}-2-oxoethyl]phosphonic acid · ligand · 2 copies · chains A, E, C, 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 · 6 copies · chains A, E, C, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.85 | 0.86 | 93 | empty |
| 2 | 1168 | 0.85 | 0.86 | 91 | SO4 |
| 3 | 1016 | 0.83 | 0.84 | 102 | GLC, FRU, SO4 |
| 4 | 1053 | 0.83 | 0.84 | 101 | GLC, SO4 |
| 5 | 1097 | 0.79 | 0.80 | 102 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2975 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2957 Ų buried · 36 hydrogen bonds · protein-protein
- A–E · 2022 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–F · 2012 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 334 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5HRO · STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE In COMPLEX WITH A DNA aptamer and an… · the same entry in another collection · chain B against B, 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 5HRO · PDBe 5HRO · UniProt P03366
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