MolNFT v1 · #121723 · protein + DNA
Structure of HIV-1 reverse transcriptase N-site complex; catalytic incorporation of aztmp to a DNA aptamer in crystal
5I3U · HIV-1 reverse transcriptase P66 subunit: “Structure of HIV-1 reverse transcriptase N-site complex; catalytic incorporation of aztmp to a DNA aptamer in…”. X-ray diffraction, 3 ligands (GLC, FRU, MG), 20 pockets (best druggability…
- PDB
- 5I3U
- 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, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase P66 subunit (EC 2.7.7.49) | protein | 550 | 33% helix, 24% strand | P03366 |
| B | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 416 | 37% helix, 21% strand | P03366 |
| C | HIV-1 reverse transcriptase P66 subunit (EC 2.7.7.49) | protein | 553 | 33% helix, 25% strand | P03366 |
| D | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 410 | 37% helix, 21% strand | P03366 |
| E, F | DNA (39-mer) | dna | 36 | — | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B, D
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains B, D
- MG · Magnesium ion · metal · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.86 | 0.87 | 93 | empty |
| 2 | 1003 | 0.86 | 0.87 | 84 | empty |
| 3 | 1031 | 0.84 | 0.85 | 98 | GLC, FRU, GOL |
| 4 | 1083 | 0.82 | 0.84 | 105 | GLC, FRU |
| 5 | 1037 | 0.77 | 0.79 | 82 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2991 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2961 Ų buried · 36 hydrogen bonds · protein-protein
- A–E · 2260 Ų buried · 28 hydrogen bonds · protein-nucleic
- C–F · 2163 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–C · 396 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nucleotide modification).
Compared structures
- 5I3U · STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE N-SITE COMPLEX; CATALYTIC INCORPORATION OF AZTMP… · 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 5I3U · PDBe 5I3U · UniProt P03366
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