Research workbench
Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer
Analyse Structure of HIV-1 reverse transcriptase bound to a novel 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
- 5D3G
- Type
- protein + DNA
- Length
- 2,001 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
- GLC, FRU, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HIV-1 reverse transcriptase P66 subunit (EC 2.7.7.49) | protein | 553 | 32% helix, 24% strand | P03366 |
| B | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 415 | 35% helix, 20% strand | P03366 |
| D | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 410 | 36% helix, 19% strand | P03366 |
| F, E | DNA aptamer (38-mer) | dna | 35 | — | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B, D
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 11 copies · chains A, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.86 | 0.89 | 81 | GOL |
| 2 | 367 | 0.81 | 0.91 | 43 | GOL |
| 3 | 413 | 0.81 | 0.89 | 60 | GOL |
| 4 | 1007 | 0.79 | 0.80 | 78 | empty |
| 5 | 256 | 0.79 | 0.92 | 30 | GOL |
Interfaces
8 interfaces between chains.
- A–B · 2985 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2972 Ų buried · 32 hydrogen bonds · protein-protein
- A–E · 2106 Ų buried · 30 hydrogen bonds · protein-nucleic
- C–F · 1982 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–C · 387 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5D3G · Structure of HIV-1 Reverse Transcriptase Bound to a Novel 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 5D3G · PDBe 5D3G · UniProt P03366
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