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Structure of HIV-1 reverse transcriptase (rt) in complex with dsdna and (+)ftc-tp
Analyse Structure of HIV-1 reverse transcriptase (rt) in complex with dsdna and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OTZ
- Type
- protein + DNA
- Length
- 998 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; P51 rt; DNA primer 20-mer; DNA template 27-mer
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.13
- UniProt
- P04585
- Ligands
- N8G, MG, SO4
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 34% 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 | 554 | 32% helix, 24% strand | P04585 |
| B | P51 rt | protein | 403 | 37% helix, 20% strand | P04585 |
| P | DNA primer 20-mer | dna | 18 | — | — |
| T | DNA template 27-mer | dna | 23 | — | — |
Ligands and binding sites
- N8G · [[(2~{S},5~{R})-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A, P, T
- MG · Magnesium ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, P, T
- GOL · Glycerol · additive · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.85 | 0.88 | 69 | empty |
| 2 | 917 | 0.85 | 0.87 | 86 | GOL |
| 3 | 420 | 0.69 | 0.80 | 38 | empty |
| 4 | 404 | 0.68 | 0.80 | 47 | empty |
| 5 | 313 | 0.66 | 0.81 | 42 | MG, N8G |
Interfaces
6 interfaces between chains.
- A–B · 3001 Ų buried · 33 hydrogen bonds · protein-protein
- A–T · 1306 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–P · 978 Ų buried · 13 hydrogen bonds · protein-nucleic
- P–T · 833 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- B–P · 103 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6OTZ · Structure of HIV-1 Reverse Transcriptase (RT) in complex with dsDNA and (+)FTC-TP · 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 6OTZ · PDBe 6OTZ · UniProt P04585
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