Research workbench
HIV-1 reverse transcriptase Y181C mutant in complex with jlj 578
Analyse HIV-1 reverse transcriptase Y181C mutant in complex with jlj 578 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DTW
- Type
- protein
- Length
- 949 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, MG, SO4
- Pockets
- 17 · best druggability 0.78
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 | 544 | 30% helix, 24% strand | P03366 |
| B | P51 rt | protein | 405 | 39% helix, 20% 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, B
- 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.78 | 0.84 | 50 | empty |
| 2 | 850 | 0.78 | 0.81 | 81 | H9Y |
| 3 | 387 | 0.70 | 0.82 | 40 | empty |
| 4 | 382 | 0.67 | 0.80 | 48 | empty |
| 5 | 288 | 0.66 | 0.82 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 2768 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6DTW · HIV-1 Reverse Transcriptase Y181C Mutant 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 6DTW · PDBe 6DTW · UniProt P03366
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