Research workbench
Crystal structure of HIV-1 reverse transcriptase in complex with RNA/DNA and datp
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
- 4PQU
- Type
- protein + DNA + RNA
- Length
- 1,993 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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
- DTP, MG, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 21% 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 | 545 | 30% helix, 23% strand | P03366 |
| B | HIV-1 reverse transcriptase, P51 subunit (EC 2.7.7.49, 2.7.7.7) | protein | 412 | 36% helix, 19% strand | P03366 |
| D | HIV-1 reverse transcriptase, P51 subunit (EC 2.7.7.49, 2.7.7.7) | protein | 413 | 34% helix, 21% strand | P03366 |
| T, E | 5'-R(*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 | 21 | — | — |
| P, F | 5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP *CP*CP*G)-3' | dna | 18 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains A, T, P, C, E, F
- MG · Magnesium ion · metal · 4 copies · chains A, P, C, F
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.87 | 0.89 | 97 | SO4 |
| 2 | 1077 | 0.86 | 0.87 | 94 | EDO, SO4 |
| 3 | 627 | 0.82 | 0.87 | 72 | SO4, GOL |
| 4 | 522 | 0.82 | 0.88 | 65 | empty |
| 5 | 917 | 0.79 | 0.81 | 84 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2980 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2907 Ų buried · 34 hydrogen bonds · protein-protein
- A–T · 1162 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–E · 1069 Ų buried · 12 hydrogen bonds · protein-nucleic
- E–F · 887 Ų buried · 97 hydrogen bonds · nucleic-nucleic
Compared structures
- 4PQU · Crystal structure of HIV-1 Reverse Transcriptase in complex with RNA/DNA and dATP · 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 4PQU · PDBe 4PQU · UniProt P03366
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