Research workbench
Crystal structure of HIV-1 reverse transcriptase (rt) in complex with a difluoromethylbenzoxazole (dfmb) pyrimidine thioether derivative, a non-nucleoside rt inhibitor (nnrti)
Analyse Crystal structure of HIV-1 reverse transcriptase (rt) in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YKN
- Type
- protein
- Length
- 967 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13
- UniProt
- P03366
- Ligands
- YKN, CA
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 557 | 32% helix, 22% strand | P03366 |
| B | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 410 | 35% helix, 19% strand | P03366 |
Ligands and binding sites
- YKN · 2-[difluoro-[(4-methyl-pyrimidinyl)-thio]methyl]-benzoxazole · ligand · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.75 | 0.82 | 61 | YKN |
| 2 | 669 | 0.74 | 0.80 | 60 | empty |
| 3 | 310 | 0.67 | 0.82 | 40 | empty |
| 4 | 417 | 0.64 | 0.78 | 46 | empty |
| 5 | 164 | 0.63 | 0.85 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2655 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2YKN · Crystal structure of HIV-1 Reverse Transcriptase (RT) in complex with a… · 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 2YKN · PDBe 2YKN · UniProt P03366
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