MolNFT v1 · #146829 · protein
Wildtype HIV-1 reverse transcriptase in complex with jlj 578
6DTX · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “Wildtype HIV-1 reverse transcriptase in complex with jlj 578”. X-ray diffraction, 1 ligand (H9Y), 14 pockets (best druggability 0.78). MolNFT v1 #146829 on GenesisL1: 3D structure, binding…
- PDB
- 6DTX
- Type
- protein
- Length
- 959 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
- H9Y
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 21% 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 | 546 | 30% helix, 23% strand | P03366 |
| B | P51 rt | protein | 413 | 37% helix, 18% strand | P03366 |
Ligands and binding sites
- H9Y · 8-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl) ethoxy]-4-fluorophenoxy}-6-fluoroindolizine-2-carbonitrile · ligand · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.78 | 0.80 | 82 | empty |
| 2 | 706 | 0.75 | 0.80 | 60 | H9Y |
| 3 | 240 | 0.68 | 0.84 | 40 | empty |
| 4 | 438 | 0.68 | 0.80 | 53 | GOL |
| 5 | 245 | 0.60 | 0.80 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 2659 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6DTX · Wildtype HIV-1 Reverse Transcriptase in complex with JLJ 578 · 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 6DTX · PDBe 6DTX · UniProt P03366
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