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Structure of HIV-1 reverse transcriptase (rt) in complex with rilpivirine and an RNase H inhibitor XZ462
Analyse Structure of HIV-1 reverse transcriptase (rt) in complex with rilpivirine and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ELI
- Type
- protein
- Length
- 972 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse transcriptase; Gag-pol polyprotein
- UniProt
- P03366
- Ligands
- T27, BA5, MG, SO4
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse transcriptase | protein | 556 | 33% helix, 23% strand | P03366 |
| B | Gag-pol polyprotein | protein | 416 | 35% helix, 20% strand | P03366 |
Ligands and binding sites
- T27 · 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile · ligand · chains A, B
- BA5 · methyl 4-azanyl-1-oxidanyl-2-oxidanylidene-1,8-naphthyridine-3-carboxylate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · chains 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.79 | 0.81 | 110 | T27 |
| 2 | 718 | 0.76 | 0.81 | 68 | empty |
| 3 | 730 | 0.72 | 0.78 | 66 | EDO |
| 4 | 191 | 0.72 | 0.89 | 23 | empty |
| 5 | 289 | 0.62 | 0.80 | 53 | empty |
Interfaces
1 interface between chains.
- A–B · 2641 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6ELI · Structure of HIV-1 reverse transcriptase (RT) in complex with rilpivirine and an RNase H… · 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 6ELI · PDBe 6ELI · UniProt P03366
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