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Crystal structure of HIV-1 reverse transcriptase (rt) in complex with janssen-R129385
Analyse Crystal structure of HIV-1 reverse transcriptase (rt) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S9E
- Type
- protein
- Length
- 979 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein [CONTAINS:REVERSE transcriptase]; Pol polyprotein [contains: reverse…
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- ADB
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pol polyprotein [CONTAINS:REVERSE transcriptase] (EC 2.7.7.49) | protein | 552 | 31% helix, 21% strand | P03366 |
| B | Pol polyprotein [contains: reverse transcriptase] (EC 2.7.7.49) | protein | 427 | 34% helix, 18% strand | P03366 |
Ligands and binding sites
- ADB · 4-[4-amino-6-(2,6-dichloro-phenoxy)-[1,3,5]triazin-2-ylamino]-benzonitrile · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.82 | 0.83 | 86 | ADB |
| 2 | 554 | 0.71 | 0.80 | 51 | empty |
| 3 | 728 | 0.70 | 0.77 | 48 | empty |
| 4 | 304 | 0.68 | 0.83 | 38 | empty |
| 5 | 274 | 0.60 | 0.79 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2473 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1S9E · Crystal structure of HIV-1 reverse transcriptase (rt) in complex with janssen-R129385 · 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 1S9E · PDBe 1S9E · UniProt P03366
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