MolNFT v1 · #14046 · protein
Crystal structure of M184V mutant HIV-1 reverse transcriptase in complex with nevirapine
1LWC: “Crystal structure of M184V mutant HIV-1 reverse transcriptase in complex with nevirapine”. X-ray diffraction, 2 ligands (NVP, PO4), 19 pockets (best druggability 0.81). MolNFT v1 #14046 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1LWC
- Type
- protein
- Length
- 909 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase
- EC
- 2.7.7.49
- UniProt
- P04585
- Ligands
- NVP, PO4
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase (EC 2.7.7.49) | protein | 507 | 33% helix, 23% strand | P04585 |
| B | HIV-1 reverse transcriptase (EC 2.7.7.49) | protein | 402 | 37% helix, 22% 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
- PO4 · Phosphate ion · ion · 2 copies · 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 | 806 | 0.81 | 0.84 | 73 | NVP |
| 2 | 605 | 0.69 | 0.78 | 66 | empty |
| 3 | 461 | 0.66 | 0.78 | 38 | empty |
| 4 | 128 | 0.62 | 0.86 | 28 | empty |
| 5 | 178 | 0.55 | 0.80 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2460 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 1LWC · Crystal structure of M184V 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 1LWC · PDBe 1LWC · UniProt P04585
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