Research workbench
Crystal structure of the HIV-1 reverse transcriptase (rt) in complex with the alkenyldiarylmethane (adam) non-nucleoside rt inhibitor dimethyl 3,3'-(6-methoxy-6-oxohex-1-ene-1,1-DIYL)BIS(5-cyano-6- methoxybenzoate).
Analyse Crystal structure of the HIV-1 reverse transcriptase (rt) in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IS9
- Type
- protein
- Length
- 970 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; Reverse transcriptase
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- P03366
- Ligands
- AC7
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 30% 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, 3.1.26.4) | protein | 554 | 28% helix, 23% strand | P03366 |
| B | Reverse transcriptase (EC 2.7.7.49, 2.7.7.7) | protein | 416 | 31% helix, 19% strand | P03366 |
Ligands and binding sites
- AC7 · dimethyl 3,3'-(6-methoxy-6-oxohex-1-ene-1,1-diyl)bis(5-cyano-6-methoxybenzoate) · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.78 | 0.82 | 62 | empty |
| 2 | 1042 | 0.78 | 0.80 | 93 | AC7 |
| 3 | 229 | 0.72 | 0.87 | 20 | empty |
| 4 | 574 | 0.68 | 0.77 | 45 | empty |
| 5 | 285 | 0.68 | 0.83 | 46 | empty |
Interfaces
1 interface between chains.
- A–B · 2647 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3IS9 · Crystal structure of the HIV-1 reverse transcriptase (RT) in complex with the… · 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 3IS9 · PDBe 3IS9 · UniProt P03366
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