Research workbench
TY3 reverse transcriptase bound to DNA/RNA
Analyse TY3 reverse transcriptase bound to DNA/RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OL8
- Type
- protein + DNA + RNA
- Length
- 1,715 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reverse TRANSCRIPTASE/RIBONUCLEASE H; 5'-R(*CP*UP*GP*AP*GP*AP*GP*AP*GP*AP*GP*GP*AP*AP*GP*A…
- EC
- 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- Q99315
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 390 | 33% helix, 20% strand | Q99315 |
| B | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 452 | 36% helix, 21% strand | Q99315 |
| C, G | 5'-R(*CP*UP*GP*AP*GP*AP*GP*AP*GP*AP*GP*GP*AP*AP*GP*AP*UP*G) -3' | rna | 17 | — | — |
| D | 5'-D(*CP*AP*TP*CP*TP*TP*CP*CP*TP*CP*TP*CP*TP*CP*TP*C)-3' | dna | 15 | — | — |
| H | 5'-D(*CP*AP*TP*CP*TP*TP*CP*CP*TP*CP*TP*CP*TP*CP*TP*C)-3' | dna | 16 | — | — |
| F | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 427 | 31% helix, 23% strand | Q99315 |
| E | Reverse TRANSCRIPTASE/RIBONUCLEASE H (EC 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 381 | 29% helix, 17% strand | Q99315 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.84 | 0.85 | 129 | empty |
| 2 | 601 | 0.83 | 0.88 | 70 | empty |
| 3 | 1027 | 0.76 | 0.78 | 92 | empty |
| 4 | 478 | 0.74 | 0.83 | 55 | empty |
| 5 | 520 | 0.66 | 0.78 | 51 | empty |
Interfaces
16 interfaces between chains.
- F–E · 1343 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1339 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 780 Ų buried · 80 hydrogen bonds · nucleic-nucleic
- C–D · 747 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- A–D · 693 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
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 Q99315
- Elsewhere: RCSB PDB 4OL8 · PDBe 4OL8 · UniProt Q99315
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