MolNFT v1 · #189320 · protein + DNA + RNA
Cryo-EM structure of E.COLI retron-EC86 in complex with its effector at 2.8 ångström
7V9X · RNA-directed DNA polymerase from retron EC86: “Cryo-EM structure of E.COLI retron-EC86 in complex with its effector at 2.8 ångström”. Electron microscopy, 17 pockets (best druggability 0.80). MolNFT v1 #189320 on GenesisL1: 3D…
- PDB
- 7V9X
- Type
- protein + DNA + RNA
- Length
- 970 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed DNA polymerase from retron EC86; Retron ST85 family effector protein; DNA…
- EC
- 2.7.7.49
- UniProt
- P23070, A0A7A0NNW9
- Pockets
- 17 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA-directed DNA polymerase from retron EC86 (EC 2.7.7.49) | protein | 314 | 52% helix, 13% strand | P23070 |
| C | Retron ST85 family effector protein | protein | 132 | 52% helix, 8% strand | A0A7A0NNW9 |
| D, G | DNA (105-mer) | dna | 39 | — | — |
| E, H | RNA (81-mer) | rna | 58 | — | — |
| F, I | RNA (14-mer) | rna | 8 | — | — |
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.80 | 0.83 | 78 | empty |
| 2 | 1147 | 0.78 | 0.80 | 87 | empty |
| 3 | 947 | 0.71 | 0.75 | 86 | empty |
| 4 | 649 | 0.65 | 0.76 | 43 | empty |
| 5 | 394 | 0.62 | 0.77 | 30 | empty |
Interfaces
19 interfaces between chains.
- B–H · 2409 Ų buried · 45 hydrogen bonds · protein-nucleic
- A–E · 2378 Ų buried · 42 hydrogen bonds · protein-nucleic
- A–D · 2277 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–G · 2245 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–B · 854 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7V9X · Cryo-EM structure of E.coli retron-Ec86 in complex with its effector at 2.8 angstrom · the same entry in another collection · chain I against I, 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 0.94
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
- Every structure of UniProt A0A7A0NNW9
- Elsewhere: RCSB PDB 7V9X · PDBe 7V9X · UniProt P23070 · UniProt A0A7A0NNW9
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