Research workbench
K65R mutant HIV-1 reverse transcriptase cross-linked to ds-DNA and complexed with tenofovir-diphosphate as the incoming nucleotide substrate
Analyse K65R mutant HIV-1 reverse transcriptase cross-linked to ds-DNA and complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JSM
- Type
- protein + DNA
- Length
- 1,011 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*A*TP*GP*GP*TP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C…
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- TNV, MG, SO4
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | DNA (5'- D(*A*TP*GP*GP*TP*CP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C P*TP*GP*TP*G)-3') | dna | 24 | — | — |
| P | DNA (5'- D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*(DDG))-3') | dna | 20 | — | — |
| A | HIV-1 reverse transcriptase P66 subunit (EC 2.7.7.49) | protein | 554 | 31% helix, 24% strand | P03366 |
| B | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.49) | protein | 413 | 31% helix, 18% strand | P03366 |
Ligands and binding sites
- TNV · [2-(6-amino-9H-purin-9-yl)-1-methylethoxy]methyl-triphosphate · ligand · chains T, P, A
- MG · Magnesium ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.87 | 0.88 | 104 | empty |
| 2 | 1144 | 0.84 | 0.85 | 96 | empty |
| 3 | 488 | 0.72 | 0.81 | 51 | empty |
| 4 | 686 | 0.71 | 0.78 | 61 | empty |
| 5 | 634 | 0.70 | 0.78 | 59 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2930 Ų buried · 28 hydrogen bonds · protein-protein
- T–A · 1357 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–A · 955 Ų buried · 12 hydrogen bonds · protein-nucleic
- T–P · 942 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- P–B · 118 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3JSM · K65R mutant HIV-1 reverse transcriptase cross-linked to DS-DNA and complexed with… · the same entry in another collection · chain T against T, 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 3JSM · PDBe 3JSM · UniProt P03366
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