Research workbench
Crystal structure of HIV-1 reverse transcriptase in complex with RNA/DNA and Nevirapine
Analyse Crystal structure of HIV-1 reverse transcriptase in complex with RNA/DNA and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PUO
- Type
- protein + DNA + RNA
- Length
- 2,011 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.901
- Source
- Human immunodeficiency virus type 1; SYNTHETIC CONSTRUCT
- Molecule
- HIV-1 Reverse Transcriptase, p66 subunit; HIV-1 Reverse Transcriptase, p51 subunit…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
- UniProt
- P03366
- Ligands
- NVP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.901 · 5 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HIV-1 Reverse Transcriptase, p66 subunit (EC 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2) | protein | 555 | 32% helix, 20% strand | P03366 |
| B, D | HIV-1 Reverse Transcriptase, p51 subunit (EC 2.7.7.49, 2.7.7.7) | protein | 412 | 37% helix, 20% strand | P03366 |
| T | 5'-R(P*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*UP*G)-3' | rna | 20 | — | — |
| E | 5'-R(P*AP*UP*GP*GP*UP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*UP*GP*UP*G)-3' | rna | 19 | — | — |
| P, F | 5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*G)-3' | dna | 19 | — | — |
Ligands and binding sites
- NVP · 11-cyclopropyl-5,11-dihydro-4-methyl-6H-dipyrido[3,2-B:2',3'-e][1,4]diazepin-6-one · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.84 | 0.85 | 92 | empty |
| 2 | 731 | 0.83 | 0.87 | 65 | empty |
| 3 | 1191 | 0.83 | 0.84 | 106 | empty |
| 4 | 190 | 0.80 | 0.95 | 24 | NVP |
| 5 | 823 | 0.79 | 0.82 | 82 | empty |
Interfaces
14 interfaces between chains.
- A–B · 2765 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2667 Ų buried · 31 hydrogen bonds · protein-protein
- T–P · 906 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- E–F · 872 Ų buried · 80 hydrogen bonds · nucleic-nucleic
- C–F · 771 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 4PUO · Crystal structure of HIV-1 reverse transcriptase in complex with RNA/DNA and nevirapine · 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 4PUO · PDBe 4PUO · UniProt P03366
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