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Crystal structure of Y188C mutant HIV-1 reverse transcriptase in complex with nevirapine
Analyse Crystal structure of Y188C 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
- 1JLF
- Type
- protein
- Length
- 943 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 rt a-chain; HIV-1 rt B-chain
- EC
- 2.7.7.49
- UniProt
- P04585
- Ligands
- NVP
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 rt a-chain (EC 2.7.7.49) | protein | 539 | 31% helix, 23% strand | P04585 |
| B | HIV-1 rt B-chain (EC 2.7.7.49) | protein | 404 | 35% 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, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.83 | 0.84 | 105 | NVP |
| 2 | 486 | 0.74 | 0.83 | 40 | empty |
| 3 | 455 | 0.65 | 0.78 | 39 | empty |
| 4 | 102 | 0.65 | 0.89 | 22 | empty |
| 5 | 258 | 0.61 | 0.80 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2566 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 1JLF · Crystal structure of Y188C 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 1JLF · PDBe 1JLF · UniProt P04585
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