MolNFT v1 · #184704 · protein + DNA
Cryo-EM structure of HIV-1 reverse transcriptase with a DNA aptamer in complex with fragment 166 at the transient P-pocket
7OZW · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “Cryo-EM structure of HIV-1 reverse transcriptase with a DNA aptamer in complex with fragment 166 at the…”. Electron microscopy, 1 ligand (3IR), 19 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 7OZW
- Type
- protein + DNA
- Length
- 995 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; DNA (37-mer)
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
- UniProt
- P03366
- Ligands
- 3IR
- Pockets
- 19 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 552 | 31% helix, 21% strand | P03366 |
| B | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 409 | 34% helix, 19% strand | P03366 |
| F | DNA (37-mer) | dna | 34 | — | — |
Ligands and binding sites
- 3IR · (1~{R},2~{R})-2-phenyl-~{N}-(1,3-thiazol-2-yl) cyclopropane-1-carboxamide · ligand · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.82 | 0.87 | 76 | empty |
| 2 | 554 | 0.79 | 0.86 | 63 | empty |
| 3 | 742 | 0.74 | 0.79 | 47 | empty |
| 4 | 379 | 0.68 | 0.81 | 44 | empty |
| 5 | 493 | 0.63 | 0.76 | 43 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2774 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 1668 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–F · 200 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 7OZW · Cryo-EM structure of HIV-1 reverse transcriptase with a DNA aptamer in complex with… · 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 7OZW · PDBe 7OZW · UniProt P03366
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.