MolNFT v1 · #159088 · protein
Crystal structure of HIV-1 reverse transcriptase in complex with 5-(2- (2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-YL)ETHOXY)PHENOXY)-7-fluoro- 2-naphthonitrile (JLJ635), a non-nucleoside inhibitor
6OE3 · HIV-1 reverse transcriptase, P66 subunit: “Crystal structure of HIV-1 reverse transcriptase in complex with 5-(2…”. X-ray diffraction, 3 ligands (M9A, MG, SO4), 17 pockets (best druggability 0.76). MolNFT v1 #159088 on GenesisL1: 3D…
- PDB
- 6OE3
- Type
- protein
- Length
- 955 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase, P66 subunit; HIV-1 reverse transcriptase, P51 subunit
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13
- UniProt
- P03366
- Ligands
- M9A, MG, SO4
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase, P66 subunit (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 546 | 31% helix, 24% strand | P03366 |
| B | HIV-1 reverse transcriptase, P51 subunit | protein | 409 | 35% helix, 19% strand | P03366 |
Ligands and binding sites
- M9A · 5-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl) ethoxy]phenoxy}-7-fluoronaphthalene-2-carbonitrile · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.76 | 0.79 | 73 | empty |
| 2 | 267 | 0.73 | 0.86 | 36 | M9A |
| 3 | 362 | 0.68 | 0.81 | 43 | empty |
| 4 | 268 | 0.67 | 0.83 | 39 | empty |
| 5 | 450 | 0.64 | 0.77 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 2449 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6OE3 · Crystal Structure of HIV-1 Reverse Transcriptase 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 6OE3 · PDBe 6OE3 · UniProt P03366
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