MolNFT v1 · #104440 · protein
Structure of a dihydroxycoumarin active-site inhibitor in complex with the RNase H domain of HIV-1 reverse transcriptase
4QAG · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “Structure of a dihydroxycoumarin active-site inhibitor in complex with the RNase H domain of HIV-1 reverse…”. X-ray diffraction, 2 ligands (F95, MN), 3 pockets (best druggability 0.47). MolNFT…
- PDB
- 4QAG
- Type
- protein
- Length
- 266 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
- UniProt
- P03366
- Ligands
- F95, MN
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 133 | 35% helix, 25% strand | P03366 |
Ligands and binding sites
- F95 · (7,8-dihydroxy-2-oxo-2H-chromen-4-yl)acetic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.47 | 0.73 | 36 | MN, F95 |
| 2 | 119 | 0.39 | 0.74 | 19 | empty |
| 3 | 125 | 0.38 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 733 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4QAG · Structure of a dihydroxycoumarin active-site inhibitor in complex with the RNASE H domain… · 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 4QAG · PDBe 4QAG · UniProt P03366
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