MolNFT v1 · #68528 · protein + DNA
K65R mutant HIV-1 reverse transcriptase cross-linked to ds-DNA and complexed with datp as the incoming nucleotide substrate
3JYT · Reverse TRANSCRIPTASE/RIBONUCLEASE H: “K65R mutant HIV-1 reverse transcriptase cross-linked to ds-DNA and complexed with datp as the incoming…”. X-ray diffraction, 3 ligands (DTP, MG, SO4), 16 pockets (best druggability 0.86).…
- PDB
- 3JYT
- Type
- protein + DNA
- Length
- 1,011 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt; DNA (5'…
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- DTP, MG, SO4
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49) | protein | 554 | 31% helix, 24% strand | P03366 |
| B | P51 rt | protein | 413 | 28% helix, 16% strand | P03366 |
| 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 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, T, P
- 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
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 803 | 0.86 | 0.89 | 92 | MG |
| 2 | 464 | 0.83 | 0.90 | 43 | empty |
| 3 | 514 | 0.73 | 0.82 | 54 | empty |
| 4 | 503 | 0.70 | 0.80 | 44 | DTP, SO4, MG |
| 5 | 557 | 0.68 | 0.78 | 57 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2956 Ų buried · 30 hydrogen bonds · protein-protein
- A–T · 1308 Ų buried · 18 hydrogen bonds · protein-nucleic
- T–P · 965 Ų buried · 100 hydrogen bonds · nucleic-nucleic
- A–P · 899 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–P · 104 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3JYT · K65R mutant HIV-1 reverse transcriptase cross-linked to DS-DNA and complexed with DATP as… · 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 3JYT · PDBe 3JYT · UniProt P03366
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