Research workbench
Wild type HIV-1 reverse transcriptase in complex with efavirenz
Analyse Wild type HIV-1 reverse transcriptase in complex with efavirenz in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IKW
- Type
- protein
- Length
- 962 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- EFZ
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pol polyprotein (EC 2.7.7.49) | protein | 557 | 31% helix, 22% strand | P03366 |
| B | Pol polyprotein (EC 2.7.7.49) | protein | 405 | 35% helix, 19% strand | P03366 |
Ligands and binding sites
- EFZ · (-)-6-chloro-4-cyclopropylethynyl-4-trifluoromethyl-1, 4-dihydro-2H-3,1-benzoxazin-2-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.80 | 0.83 | 76 | EFZ |
| 2 | 800 | 0.73 | 0.78 | 70 | empty |
| 3 | 300 | 0.67 | 0.82 | 38 | empty |
| 4 | 279 | 0.63 | 0.80 | 32 | empty |
| 5 | 152 | 0.50 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2654 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1IKW · Wild Type HIV-1 Reverse Transcriptase in Complex with Efavirenz · 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 P03366
- Elsewhere: RCSB PDB 1IKW · PDBe 1IKW · UniProt P03366
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