Research workbench
Crystal structure of a dihydroxycoumarin RNase H active-site inhibitor in complex with HIV-1 reverse transcriptase
Analyse Crystal structure of a dihydroxycoumarin RNase H active-site inhibitor in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HBM
- Type
- protein
- Length
- 965 residues
- Chains
- 2
- 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, 3.1.13.2
- UniProt
- P03366
- Ligands
- NVP, F95, MN
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% 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, 3.1.13.2) | protein | 552 | 33% helix, 24% strand | P03366 |
| B | P51 rt | protein | 413 | 35% helix, 19% strand | P03366 |
Ligands and binding sites
- NVP · 11-cyclopropyl-5,11-dihydro-4-methyl-6H-dipyrido[3,2-B:2',3'-e][1,4]diazepin-6-one · ligand · chains A
- F95 · (7,8-dihydroxy-2-oxo-2H-chromen-4-yl)acetic acid · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.81 | 0.82 | 90 | NVP |
| 2 | 1063 | 0.80 | 0.81 | 95 | empty |
| 3 | 756 | 0.72 | 0.78 | 67 | empty |
| 4 | 314 | 0.69 | 0.83 | 40 | empty |
| 5 | 152 | 0.48 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2532 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5HBM · Crystal Structure of a Dihydroxycoumarin RNase H Active-Site Inhibitor 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 5HBM · PDBe 5HBM · UniProt P03366
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.