MolNFT v1 · #15505 · protein + DNA
HIV-1 reverse transcriptase crosslinked to pre-translocation aztmp- terminated DNA (complex N)
1N6Q · 5'-D(*AP*T*GP*CP*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*…: “HIV-1 reverse transcriptase crosslinked to pre-translocation aztmp- terminated DNA (complex N)”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.83).…
- PDB
- 1N6Q
- Type
- protein + DNA
- Length
- 1,467 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*T*GP*CP*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*…
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'-D(*AP*T*GP*CP*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP* GP*GP*GP*AP*CP*TP*GP*TP*G)-3' | dna | 23 | — | — |
| P | 5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*AP*(ATM))-3' | dna | 21 | — | — |
| A | Reverse transcriptase (EC 2.7.7.49) | protein | 558 | 32% helix, 22% strand | P03366 |
| B | Reverse transcriptase (EC 2.7.7.49) | protein | 429 | 33% helix, 17% strand | P03366 |
| L | Monoclonal antibody (light chain) | protein | 211 | 4% helix, 46% strand | — |
| H | Monoclonal antibody (heavy chain) | protein | 225 | 3% helix, 51% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains P, A, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.83 | 0.85 | 77 | empty |
| 2 | 545 | 0.82 | 0.88 | 56 | empty |
| 3 | 384 | 0.80 | 0.89 | 58 | empty |
| 4 | 868 | 0.77 | 0.80 | 63 | empty |
| 5 | 311 | 0.71 | 0.85 | 41 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2915 Ų buried · 38 hydrogen bonds · protein-protein
- L–H · 1844 Ų buried · 12 hydrogen bonds · protein-protein
- T–A · 1345 Ų buried · 13 hydrogen bonds · protein-nucleic
- P–A · 1141 Ų buried · 18 hydrogen bonds · protein-nucleic
- T–P · 963 Ų buried · 91 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, nucleotide modification).
Compared structures
- 1N6Q · HIV-1 Reverse Transcriptase Crosslinked to pre-translocation AZTMP-terminated DNA… · 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 1N6Q · PDBe 1N6Q · UniProt P03366
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