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Crystal structure of HIV-1 reverse transcriptase (rt) cross-linked with azt-terminated DNA
Analyse Crystal structure of HIV-1 reverse transcriptase (rt) cross-linked with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V6D
- 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; DNA…
- EC
- 2.7.7.49, 2.7.7.7
- UniProt
- P03366
- Pockets
- 20 · best druggability 0.87
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) | protein | 555 | 32% helix, 24% strand | P03366 |
| B, D | HIV-1 reverse transcriptase P51 subunit (EC 2.7.7.49, 2.7.7.7) | protein | 412 | 35% helix, 20% strand | P03366 |
| C | HIV-1 reverse transcriptase P66 subunit (EC 2.7.7.49, 2.7.7.7) | protein | 554 | 32% helix, 22% strand | P03366 |
| T, E | DNA (5'- D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP* CP*TP*GP*TP*G)-3') | dna | 24 | — | — |
| P, F | DNA (5'- D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*(ATM))-3') | dna | 20 | — | — |
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 | 1010 | 0.87 | 0.89 | 99 | empty |
| 2 | 604 | 0.83 | 0.88 | 66 | empty |
| 3 | 353 | 0.81 | 0.90 | 32 | empty |
| 4 | 419 | 0.79 | 0.87 | 56 | empty |
| 5 | 1113 | 0.76 | 0.78 | 89 | empty |
Interfaces
13 interfaces between chains.
- C–D · 2992 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2958 Ų buried · 37 hydrogen bonds · protein-protein
- A–T · 1350 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–E · 1267 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–F · 1003 Ų buried · 18 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3V6D · Crystal structure of HIV-1 reverse transcriptase (RT) cross-linked with AZT-terminated DNA · 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 3V6D · PDBe 3V6D · UniProt P03366
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