Research workbench
Crystal structure of V108I mutant HIV-1 reverse transcriptase in complex with nevirapine
Analyse Crystal structure of V108I mutant HIV-1 reverse transcriptase 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
- 1S1X
- Type
- protein
- Length
- 943 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse transcriptase
- EC
- 2.7.7.49
- UniProt
- P04585
- Ligands
- NVP
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase (EC 2.7.7.49) | protein | 546 | 32% helix, 22% strand | P04585 |
| B | Reverse transcriptase (EC 2.7.7.49) | protein | 397 | 38% helix, 21% strand | P04585 |
Ligands and binding sites
- NVP · 11-cyclopropyl-5,11-dihydro-4-methyl-6H-dipyrido[3,2-B:2',3'-e][1,4]diazepin-6-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.80 | 0.81 | 90 | NVP |
| 2 | 679 | 0.72 | 0.79 | 59 | empty |
| 3 | 427 | 0.63 | 0.77 | 40 | empty |
| 4 | 374 | 0.59 | 0.76 | 31 | empty |
| 5 | 179 | 0.57 | 0.80 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 2700 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 1S1X · Crystal structure of V108I mutant HIV-1 reverse transcriptase in complex with nevirapine · 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 P04585
- Elsewhere: RCSB PDB 1S1X · PDBe 1S1X · UniProt P04585
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.