Research workbench
Crystal structure of HIV-1 reverse transcriptase in complex with GF128590.
Analyse Crystal structure of HIV-1 reverse transcriptase in complex with GF128590. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DLE
- Type
- protein
- Length
- 938 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- P04585
- Ligands
- GFA
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 535 | 31% helix, 25% strand | P04585 |
| B | P51 rt | protein | 403 | 35% helix, 21% strand | P04585 |
Ligands and binding sites
- GFA · 2-[4-chloro-2-(phenylcarbonyl)phenoxy]-N-phenylacetamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.80 | 0.81 | 85 | GFA |
| 2 | 497 | 0.76 | 0.84 | 42 | empty |
| 3 | 354 | 0.61 | 0.78 | 33 | empty |
| 4 | 392 | 0.59 | 0.76 | 39 | empty |
| 5 | 172 | 0.59 | 0.82 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2564 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 3DLE · Crystal structure of hiv-1 reverse transcriptase in complex with GF128590. · 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 3DLE · PDBe 3DLE · UniProt P04585
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