Research workbench
Crystal structure of HIV-1 reverse transcriptase Y181C variant in complex with (E)-4-((4-((4-(2-cyanovinyl)-2,6-DIMETHYLPHENYL)AMINO)- 6-(3-morpholinopropoxy)-1,3,5-triazin-2-YL)AMINO)BENZONITRILE (JLJ564)
Analyse Crystal structure of HIV-1 reverse transcriptase Y181C variant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SO2
- Type
- protein
- Length
- 940 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
- 9W3
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 32% 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 | 540 | 29% helix, 24% strand | P03366 |
| B | P51 rt | protein | 400 | 36% helix, 20% strand | P03366 |
Ligands and binding sites
- 9W3 · 4-[(4-{4-[(E)-2-cyanoethenyl]-2,6-dimethylanilino}-6-[3-(morpholin-4-yl)propoxy]-1,3,5-triazin-2-yl) amino]benzonitrile · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.79 | 0.80 | 87 | 9W3 |
| 2 | 702 | 0.77 | 0.81 | 66 | empty |
| 3 | 204 | 0.61 | 0.82 | 21 | empty |
| 4 | 207 | 0.60 | 0.81 | 30 | empty |
| 5 | 245 | 0.60 | 0.80 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 2622 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 7SO2 · Crystal Structure of HIV-1 Reverse Transcriptase Y181C Variant 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 7SO2 · PDBe 7SO2 · UniProt P03366
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