MolNFT v1 · #15477 · protein + DNA
HIV-1 reverse transcriptase crosslinked to post-translocation aztmp- terminated DNA (complex P)
1N5Y · 5'-D(*AP*TP*GP*C*TP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*…: “HIV-1 reverse transcriptase crosslinked to post-translocation aztmp- terminated DNA (complex P)”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.85).…
- PDB
- 1N5Y
- Type
- protein + DNA
- Length
- 1,464 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*TP*GP*C*TP*AP*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 0.85
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'-D(*AP*TP*GP*C*TP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP* GP*GP*GP*AP*CP*TP*GP*TP*G)-3' | dna | 21 | — | — |
| P | 5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG) P*CP*GP*CP*CP*(ATM))-3' | dna | 20 | — | — |
| A | Reverse transcriptase (EC 2.7.7.49) | protein | 558 | 31% 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 | 5% helix, 47% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
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 | 1040 | 0.85 | 0.86 | 94 | MG |
| 2 | 984 | 0.84 | 0.85 | 99 | empty |
| 3 | 1051 | 0.78 | 0.80 | 81 | empty |
| 4 | 322 | 0.70 | 0.84 | 39 | empty |
| 5 | 381 | 0.64 | 0.79 | 33 | empty |
Interfaces
9 interfaces between chains.
- A–B · 3007 Ų buried · 36 hydrogen bonds · protein-protein
- L–H · 1802 Ų buried · 9 hydrogen bonds · protein-protein
- T–A · 1142 Ų buried · 11 hydrogen bonds · protein-nucleic
- P–A · 1003 Ų buried · 12 hydrogen bonds · protein-nucleic
- T–P · 920 Ų buried · 107 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, nucleotide modification).
Compared structures
- 1N5Y · HIV-1 Reverse Transcriptase Crosslinked to Post-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 1N5Y · PDBe 1N5Y · UniProt P03366
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