MolNFT v1 · #19964 · protein + DNA
Crystal structure of HIV-1 reverse transcriptase covalently tethered to DNA template-primer solved to 2.8 ångströms
1R0A · 5'-D(*A*TP*GP*CP*AP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*AP*AP*CP*…: “Crystal structure of HIV-1 reverse transcriptase covalently tethered to DNA template-primer solved to 2.8…”. X-ray diffraction, 2 ligands (GLC, MG), 19 pockets (best…
- PDB
- 1R0A
- Type
- protein + DNA
- Length
- 1,467 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*A*TP*GP*CP*AP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*AP*AP*CP*…
- EC
- 2.7.7.49
- UniProt
- P03366
- Ligands
- GLC, MG
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | 5'-D(*A*TP*GP*CP*AP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*AP*AP*CP* AP*GP*GP*GP*AP*CP*GP*GP*T)-3' | dna | 24 | — | — |
| P | 5'-D(*C*CP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*AP*GP*CP*GP*CP* CP*GP*(2DA))-3' | dna | 20 | — | — |
| A | Reverse transcriptase (EC 2.7.7.49) | protein | 558 | 31% helix, 21% strand | P03366 |
| B | Reverse transcriptase (EC 2.7.7.49) | protein | 429 | 34% helix, 18% strand | P03366 |
| L | Monoclonal antibody (light chain) | protein | 211 | 5% helix, 50% strand | — |
| H | Monoclonal antibody (heavy chain) | protein | 225 | 5% helix, 52% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains L, H
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains P, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.87 | 0.88 | 104 | MG, GOL |
| 2 | 965 | 0.86 | 0.87 | 96 | empty |
| 3 | 886 | 0.78 | 0.80 | 62 | empty |
| 4 | 605 | 0.70 | 0.78 | 57 | empty |
| 5 | 259 | 0.69 | 0.85 | 41 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2917 Ų buried · 32 hydrogen bonds · protein-protein
- L–H · 1829 Ų buried · 12 hydrogen bonds · protein-protein
- T–A · 1547 Ų buried · 19 hydrogen bonds · protein-nucleic
- P–A · 976 Ų buried · 13 hydrogen bonds · protein-nucleic
- T–P · 923 Ų buried · 83 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 1R0A · Crystal structure of HIV-1 reverse transcriptase covalently tethered to 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 1R0A · PDBe 1R0A · UniProt P03366
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