Research workbench
Crystal structure of HIV-1 reverse transcriptase in complex with 4-(3- chloro-5-cyanophenoxy)-3-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)- YL)ETHOXY)PHENYL sulfurofluoridate (JLJ702)
Analyse Crystal structure of HIV-1 reverse transcriptase in complex with 4-(3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KRD
- Type
- protein
- Length
- 953 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 reverse transcriptase, P66 subunit; HIV-1 reverse transcriptase, P51 subunit
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13
- UniProt
- P03366
- Ligands
- X2S
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 reverse transcriptase, P66 subunit (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 545 | 31% helix, 24% strand | P03366 |
| B | HIV-1 reverse transcriptase, P51 subunit | protein | 408 | 35% helix, 18% strand | P03366 |
Ligands and binding sites
- X2S · 4-(3-chloro-5-cyanophenoxy)-3-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenyl sulfurofluoridate · ligand · 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.75 | 0.79 | 73 | empty |
| 2 | 333 | 0.71 | 0.84 | 48 | X2S |
| 3 | 577 | 0.66 | 0.76 | 59 | empty |
| 4 | 296 | 0.65 | 0.81 | 42 | empty |
| 5 | 275 | 0.65 | 0.82 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 2396 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7KRD · Crystal Structure of HIV-1 Reverse Transcriptase in Complex with… · 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 7KRD · PDBe 7KRD · UniProt P03366
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