MolNFT v1 · #122834 · protein
Crystal structure of a hydroxypyridone carboxylic acid active-site RNase H inhibitor in complex with HIV reverse transcriptase
5J1E · HIV-1 reverse transcriptase P66 domain: “Crystal structure of a hydroxypyridone carboxylic acid active-site RNase H inhibitor in complex with HIV…”. X-ray diffraction, 2 ligands (6FT, MG), 20 pockets (best druggability 0.80). MolNFT…
- PDB
- 5J1E
- Type
- protein
- Length
- 1,887 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase P66 domain; HIV-1 reverse transcriptase P51 domain
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- P03366
- Ligands
- 6FT, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase P66 domain (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 541 | 32% helix, 24% strand | P03366 |
| B | HIV-1 reverse transcriptase P51 domain (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 405 | 35% helix, 19% strand | P03366 |
| C | HIV-1 reverse transcriptase P66 domain (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 548 | 32% helix, 24% strand | P03366 |
| D | HIV-1 reverse transcriptase P51 domain (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 393 | 37% helix, 20% strand | P03366 |
Ligands and binding sites
- 6FT · 5-hydroxy-4-oxo-1-[(4'-sulfamoyl[1,1'-biphenyl]-4-yl)methyl]-1,4-dihydropyridine-3-carboxylic acid · ligand · chains C
- MG · Magnesium ion · metal · 3 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.80 | 0.82 | 85 | empty |
| 2 | 1063 | 0.77 | 0.79 | 84 | MG |
| 3 | 576 | 0.73 | 0.81 | 44 | empty |
| 4 | 419 | 0.69 | 0.80 | 37 | empty |
| 5 | 491 | 0.69 | 0.79 | 42 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2950 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2791 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 751 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 617 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5J1E · Crystal Structure of a Hydroxypyridone Carboxylic Acid Active-Site RNase H Inhibitor in… · the same entry in another collection · chain D against D, 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 5J1E · PDBe 5J1E · UniProt P03366
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