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Crystal structure of HIV-1 reverse transcriptase (rt) with DNA and a nucleoside triphosphate mimic alpha-carboxy nucleoside phosphonate inhibitor
Analyse Crystal structure of HIV-1 reverse transcriptase (rt) with DNA and a nucleoside… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R5P
- Type
- protein + DNA
- Length
- 2,021 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
- 3JY, GLC, FRU, MG, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 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, 23% strand | P03366 |
| 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 | 554 | 33% helix, 22% strand | P03366 |
| B, D | HIV-1 reverse transcriptase, P51 subunit (EC 2.7.7.49, 2.7.7.7) | protein | 412 | 35% helix, 19% strand | P03366 |
| T, E | 5'-D(*TP*GP*GP*AP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP *GP*GP*AP*CP*TP*G)-3' | dna | 24 | — | — |
| P, F | 5'-D(*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*G)-3' | dna | 20 | — | — |
Ligands and binding sites
- 3JY · [(1R)-2-methoxy-1-{[(1S,3R)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}-2-oxoethyl]phosphonic acid · ligand · 2 copies · chains A, T, P, C, E, F
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains B, D
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains B, D
- MG · Magnesium ion · metal · 6 copies · chains A, T, C, B, D
- SO4 · Sulfate ion · ion · chains C, D
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 | 631 | 0.84 | 0.89 | 64 | empty |
| 2 | 396 | 0.82 | 0.91 | 40 | empty |
| 3 | 446 | 0.82 | 0.90 | 48 | SO4 |
| 4 | 651 | 0.82 | 0.86 | 63 | empty |
| 5 | 500 | 0.81 | 0.88 | 51 | empty |
Interfaces
13 interfaces between chains.
- C–D · 2950 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2946 Ų buried · 35 hydrogen bonds · protein-protein
- A–T · 1416 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–E · 1336 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–F · 990 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4R5P · Crystal structure of HIV-1 reverse transcriptase (RT) with DNA and a nucleoside… · 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 4R5P · PDBe 4R5P · UniProt P03366
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