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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
- 2VG6
- 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, 3.1.26.4
- UniProt
- P03366
- Ligands
- NNB
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 19% 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 | 548 | 31% helix, 20% strand | P03366 |
| B | P51 rt | protein | 401 | 36% helix, 18% strand | P03366 |
Ligands and binding sites
- NNB · O-[2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)ethyl] (4-bromophenyl)thiocarbamate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.81 | 0.82 | 98 | NNB |
| 2 | 778 | 0.75 | 0.79 | 71 | empty |
| 3 | 72 | 0.63 | 0.91 | 19 | empty |
| 4 | 377 | 0.63 | 0.78 | 46 | empty |
| 5 | 212 | 0.59 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2583 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 2VG6 · 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 2VG6 · PDBe 2VG6 · UniProt P03366
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