MolNFT v1 · #11394 · protein
Crystal structure of Y181C mutant HIV-1 reverse transcriptase in complex with nevirapine
1JLB · HIV-1 rt a-chain: “Crystal structure of Y181C mutant HIV-1 reverse transcriptase in complex with nevirapine”. X-ray diffraction, 1 ligand (NVP), 13 pockets (best druggability 0.81). MolNFT v1 #11394 on GenesisL1: 3D structure…
- PDB
- 1JLB
- Type
- protein
- Length
- 955 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
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 rt a-chain (EC 2.7.7.49) | protein | 550 | 33% helix, 25% strand | P04585 |
| B | HIV-1 rt B-chain (EC 2.7.7.49) | protein | 405 | 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.81 | 0.82 | 90 | NVP |
| 2 | 481 | 0.76 | 0.84 | 43 | empty |
| 3 | 669 | 0.69 | 0.77 | 57 | empty |
| 4 | 414 | 0.63 | 0.77 | 35 | empty |
| 5 | 101 | 0.62 | 0.88 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2660 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 1JLB · Crystal structure of Y181C mutant HIV-1 reverse transcriptase in complex with nevirapine · the same entry in another collection · chain B against B, 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 1JLB · PDBe 1JLB · UniProt P04585
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.