MolNFT v1 · #139682 · protein + DNA
HIV-1 reverse transcriptase Q151M:DNA:DGTP ternary complex
5XN2 · Pol protein: “HIV-1 reverse transcriptase Q151M:DNA:DGTP ternary complex”. X-ray diffraction, 4 ligands (DGT, GLC, FRU), 20 pockets (best druggability 0.86). MolNFT v1 #139682 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5XN2
- Type
- protein + DNA
- Length
- 1,989 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol protein; 38-mer DNA aptamer
- UniProt
- D3XFN7
- Ligands
- DGT, GLC, FRU, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pol protein | protein | 551 | 33% helix, 24% strand | D3XFN7 |
| B, D | Pol protein | protein | 407 | 34% helix, 20% strand | D3XFN7 |
| E | 38-mer DNA aptamer | dna | 35 | — | — |
| F | 38-mer DNA aptamer | dna | 38 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, E, C, F
- GLC · alpha-D-glucopyranose · sugar · chains B
- FRU · beta-D-fructofuranose · sugar · chains B, E
- MG · Magnesium ion · metal · 2 copies · chains A, C
- GOL · Glycerol · additive · 4 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.86 | 0.87 | 115 | GOL |
| 2 | 904 | 0.83 | 0.85 | 98 | GLC, FRU, GOL |
| 3 | 339 | 0.82 | 0.92 | 40 | GOL |
| 4 | 515 | 0.76 | 0.84 | 59 | empty |
| 5 | 286 | 0.74 | 0.87 | 35 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2948 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2944 Ų buried · 33 hydrogen bonds · protein-protein
- C–F · 1993 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–E · 1862 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 807 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5XN2 · HIV-1 reverse transcriptase Q151M:DNA:dGTP ternary complex · the same entry in another collection · chain C against C, 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 D3XFN7
- Elsewhere: RCSB PDB 5XN2 · PDBe 5XN2 · UniProt D3XFN7
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