Research workbench
Structure of HIV-1 reverse transcriptase in complex with DNA and indopy-1
Analyse Structure of HIV-1 reverse transcriptase in complex with DNA and indopy-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O9E
- Type
- protein + DNA
- Length
- 2,001 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse transcriptase P66; Reverse transcriptase P51; DNA (38-mer)
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.4.23.16
- UniProt
- P03366
- Ligands
- IY1, GLC, FRU, SO4, NH4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Reverse transcriptase P66 (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 553 | 33% helix, 24% strand | P03366 |
| B | Reverse transcriptase P51 (EC 3.4.23.16) | protein | 415 | 36% helix, 20% strand | P03366 |
| D | Reverse transcriptase P51 (EC 3.4.23.16) | protein | 410 | 35% helix, 20% strand | P03366 |
| F, E | DNA (38-mer) | dna | 35 | — | — |
Ligands and binding sites
- IY1 · 5-methyl-1-(4-nitrophenyl)-2-oxo-2,5-dihydro-1H-pyrido[3,2-b]indole-3-carbonitrile · ligand · 2 copies · chains C, F, A, E
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B, D
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
- NH4 · Ammonium ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 3 copies · chains B, C, A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B
- PG4 · Tetraethylene glycol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.87 | 0.90 | 97 | empty |
| 2 | 825 | 0.86 | 0.88 | 89 | SO4, GOL |
| 3 | 368 | 0.82 | 0.91 | 47 | empty |
| 4 | 783 | 0.79 | 0.83 | 70 | empty |
| 5 | 238 | 0.73 | 0.87 | 30 | empty |
Interfaces
8 interfaces between chains.
- A–B · 3011 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2984 Ų buried · 33 hydrogen bonds · protein-protein
- A–E · 2124 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–F · 2073 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 432 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6O9E · Structure of HIV-1 Reverse Transcriptase in complex with DNA and INDOPY-1 · 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 6O9E · PDBe 6O9E · UniProt P03366
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