MolNFT v1 · #136506 · protein
Crystal structure of a 2-hydroxyisoquinoline-1,3-dione RNase H active site inhibitor with multiple binding modes to HIV reverse transcriptase
5UV5 · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “Crystal structure of a 2-hydroxyisoquinoline-1,3-dione RNase H active site inhibitor with multiple binding…”. X-ray diffraction, 2 ligands (Y55, MN), 20 pockets (best druggability 0.81). MolNFT…
- PDB
- 5UV5
- Type
- protein
- Length
- 1,873 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13
- UniProt
- P03366
- Ligands
- Y55, MN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 22% 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) | protein | 534 | 31% helix, 23% strand | P03366 |
| B | P51 rt | protein | 400 | 34% helix, 20% strand | P03366 |
| C | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 546 | 32% helix, 22% strand | P03366 |
| D | P51 rt | protein | 393 | 38% helix, 20% strand | P03366 |
Ligands and binding sites
- Y55 · 7-(furan-2-yl)-2-hydroxyisoquinoline-1,3(2H,4H)-dione · ligand · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 4 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.81 | 0.84 | 100 | Y55 |
| 2 | 343 | 0.75 | 0.86 | 50 | empty |
| 3 | 541 | 0.72 | 0.80 | 50 | empty |
| 4 | 649 | 0.71 | 0.78 | 47 | empty |
| 5 | 801 | 0.71 | 0.76 | 75 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2930 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2811 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 689 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 536 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5UV5 · Crystal Structure of a 2-Hydroxyisoquinoline-1,3-dione RNase H Active Site Inhibitor 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 5UV5 · PDBe 5UV5 · UniProt P03366
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