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Crystal structure of HIV-1 reverse transcriptase in complex with N1-heterocycle pyrimidinedione non-nucleoside inhibitor
Analyse Crystal structure of HIV-1 reverse transcriptase in complex with N1-heterocycle… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LAK
- 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
- KR1, SO4, CL
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% 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 | 38% helix, 18% strand | P04585 |
Ligands and binding sites
- KR1 · 3-({3-[(2-amino-6-fluoropyridin-4-yl)methyl]-5-(1-methylethyl)-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl}carbonyl)-5-methylbenzonitrile · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.75 | 0.79 | 83 | empty |
| 2 | 305 | 0.75 | 0.87 | 39 | KR1 |
| 3 | 440 | 0.71 | 0.81 | 37 | empty |
| 4 | 273 | 0.68 | 0.83 | 38 | empty |
| 5 | 205 | 0.59 | 0.81 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2853 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3LAK · Crystal structure of HIV-1 reverse transcriptase in complex with N1-heterocycle… · 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 3LAK · PDBe 3LAK · UniProt P04585
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