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Structure of HIV-1 reverse transcriptase (rt) in complex with dsdna and D4T
Analyse Structure of HIV-1 reverse transcriptase (rt) in complex with dsdna and D4T in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WPJ
- Type
- protein + DNA
- Length
- 992 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt; DNA primer 21-mer; DNA template 27-mer
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.-.-
- UniProt
- P04585
- Ligands
- D4T, MG, SO4
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.13) | protein | 557 | 33% helix, 23% strand | P04585 |
| B | P51 rt (EC 2.7.7.-, 3.1.-.-) | protein | 394 | 38% helix, 21% strand | P04585 |
| P | DNA primer 21-mer | dna | 18 | — | — |
| T | DNA template 27-mer | dna | 23 | — | — |
Ligands and binding sites
- D4T · 2',3'-dehydro-2',3'-deoxy-thymidine 5'-triphosphate · ligand · chains A, P, T
- MG · Magnesium ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.87 | 0.89 | 85 | empty |
| 2 | 522 | 0.84 | 0.90 | 56 | empty |
| 3 | 488 | 0.71 | 0.80 | 39 | empty |
| 4 | 541 | 0.71 | 0.80 | 51 | empty |
| 5 | 420 | 0.71 | 0.82 | 43 | D4T |
Interfaces
6 interfaces between chains.
- A–B · 2984 Ų buried · 36 hydrogen bonds · protein-protein
- A–T · 1283 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–P · 1045 Ų buried · 13 hydrogen bonds · protein-nucleic
- P–T · 845 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- B–P · 106 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6WPJ · Structure of HIV-1 Reverse Transcriptase (RT) in complex with dsDNA and d4T · 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 P04585
- Elsewhere: RCSB PDB 6WPJ · PDBe 6WPJ · UniProt P04585
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