MolNFT v1 · #189319 · protein + DNA + RNA
Cryo-EM structure of E.COLI retron-EC86 (rt-msdna-RNA) at 3.2 ångström
7V9U · RNA-directed DNA polymerase from retron EC86: “Cryo-EM structure of E.COLI retron-EC86 (rt-msdna-RNA) at 3.2 ångström”. Electron microscopy, 10 pockets (best druggability 0.80). MolNFT v1 #189319 on GenesisL1: 3D structure, binding…
- PDB
- 7V9U
- Type
- protein + DNA + RNA
- Length
- 827 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed DNA polymerase from retron EC86; DNA (105-mer); RNA (81-mer); RNA…
- EC
- 2.7.7.49
- UniProt
- P23070
- Pockets
- 10 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA-directed DNA polymerase from retron EC86 (EC 2.7.7.49) | protein | 309 | 49% helix, 14% strand | P23070 |
| D, C | DNA (105-mer) | dna | 39 | — | — |
| E | RNA (81-mer) | rna | 57 | — | — |
| F, H | RNA (5'-R(P*CP*GP*UP*AP*AP*GP*GP*G)-3') | rna | 8 | — | — |
| G | RNA (81-mer) | rna | 58 | — | — |
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.80 | 0.82 | 71 | empty |
| 2 | 1133 | 0.79 | 0.81 | 84 | empty |
| 3 | 165 | 0.47 | 0.77 | 15 | empty |
| 4 | 142 | 0.44 | 0.77 | 16 | empty |
| 5 | 85 | 0.43 | 0.80 | 20 | empty |
Interfaces
15 interfaces between chains.
- B–G · 2494 Ų buried · 55 hydrogen bonds · protein-nucleic
- A–E · 2452 Ų buried · 45 hydrogen bonds · protein-nucleic
- A–D · 2223 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–C · 2184 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 776 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7V9U · Cryo-EM structure of E.coli retron-Ec86 (RT-msDNA-RNA) at 3.2 angstrom · the same entry in another collection · chain H against H, TM-score 1.00
- P23070 · AlphaFold monomer V2.0 prediction for RNA-directed DNA polymerase from retron EC86… · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P23070
- Elsewhere: RCSB PDB 7V9U · PDBe 7V9U · UniProt P23070
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