Research workbench
Cryo-EM structure of HIV-1 reverse transcriptase with a DNA aptamer in complex with fragment F04 at the transient P-pocket
Analyse Cryo-EM structure of HIV-1 reverse transcriptase with a DNA aptamer in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P15
- Type
- protein + DNA
- Length
- 1,003 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
- 4OI
- Pockets
- 19 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 33% helix, 18% 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 | 553 | 32% helix, 19% 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 | 416 | 34% helix, 17% strand | P03366 |
| F | DNA (37-mer) | dna | 34 | — | — |
Ligands and binding sites
- 4OI · (1~{R},2~{R})-~{N}-(1~{H}-pyrazol-4-yl)-2-pyridin-3-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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.83 | 0.88 | 73 | empty |
| 2 | 367 | 0.82 | 0.91 | 51 | empty |
| 3 | 941 | 0.76 | 0.78 | 88 | 4OI |
| 4 | 448 | 0.66 | 0.78 | 38 | empty |
| 5 | 308 | 0.66 | 0.81 | 61 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2773 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 1783 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–F · 216 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 7P15 · 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 7P15 · PDBe 7P15 · UniProt P03366
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