Research workbench
Structure of HIV-1 reverse transcriptase in complex with a DNA aptamer, azttp, and CA(2+) ion
Analyse Structure of HIV-1 reverse transcriptase in complex with a DNA aptamer, azttp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I42
- Type
- protein + DNA
- Length
- 2,002 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
- AZT, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 33% 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 | 554 | 31% helix, 22% strand | P03366 |
| B, D | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 412 | 36% helix, 19% strand | P03366 |
| E, F | DNA (38-mer) | dna | 35 | — | — |
Ligands and binding sites
- AZT · 3'-azido-3'-deoxythymidine-5'-triphosphate · ligand · 2 copies · chains A, E, C, F
- CA · Calcium ion · metal · 2 copies · chains A, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.86 | 0.88 | 112 | empty |
| 2 | 713 | 0.82 | 0.85 | 60 | empty |
| 3 | 345 | 0.81 | 0.91 | 40 | empty |
| 4 | 390 | 0.81 | 0.90 | 50 | empty |
| 5 | 836 | 0.78 | 0.81 | 70 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2987 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2947 Ų buried · 34 hydrogen bonds · protein-protein
- A–E · 1957 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–F · 1929 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–C · 270 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5I42 · Structure of HIV-1 Reverse Transcriptase in complex with a DNA aptamer, AZTTP, and CA(2+)… · 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 5I42 · PDBe 5I42 · UniProt P03366
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.