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Crystal structures of HIV-1 reverse transcriptase complexes with thiocarbamate non-nucleoside inhibitors
Analyse Crystal structures of HIV-1 reverse transcriptase complexes with thiocarbamate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VG5
- Type
- protein
- Length
- 952 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, 3.1.26.4
- UniProt
- P03366
- Ligands
- NNC
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 551 | 32% helix, 21% strand | P03366 |
| B | P51 rt | protein | 401 | 36% helix, 19% strand | P03366 |
Ligands and binding sites
- NNC · O-[2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)ethyl] (4-chlorophenyl)thiocarbamate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.80 | 0.82 | 82 | NNC |
| 2 | 387 | 0.66 | 0.79 | 44 | empty |
| 3 | 259 | 0.65 | 0.82 | 39 | empty |
| 4 | 418 | 0.65 | 0.78 | 39 | empty |
| 5 | 348 | 0.62 | 0.78 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 2624 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 2VG5 · Crystal structures of HIV-1 reverse transcriptase complexes with thiocarbamate… · 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 2VG5 · PDBe 2VG5 · UniProt P03366
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