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Crystal structure of HIV-1 reverse transcriptase in complex with N1-ethyl pyrimidinedione non-nucleoside inhibitor
Analyse Crystal structure of HIV-1 reverse transcriptase in complex with N1-ethyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LAL
- Type
- protein
- Length
- 956 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV reverse transcriptase
- EC
- 2.7.7.49
- UniProt
- P04585
- Ligands
- KRV, SO4
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV reverse transcriptase (EC 2.7.7.49) | protein | 553 | 32% helix, 24% strand | P04585 |
| B | HIV reverse transcriptase (EC 2.7.7.49) | protein | 403 | 39% helix, 19% strand | P04585 |
Ligands and binding sites
- KRV · 3-{[3-ethyl-5-(1-methylethyl)-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl]carbonyl}-5-methylbenzonitrile · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.82 | 0.83 | 94 | KRV |
| 2 | 404 | 0.69 | 0.81 | 30 | empty |
| 3 | 249 | 0.66 | 0.83 | 31 | empty |
| 4 | 201 | 0.61 | 0.82 | 33 | empty |
| 5 | 122 | 0.57 | 0.83 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2861 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3LAL · Crystal structure of HIV-1 reverse transcriptase in complex with N1-ethyl pyrimidinedione… · 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 3LAL · PDBe 3LAL · UniProt P04585
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