Research workbench
cryoEM structure DrdV-DNA complex
Analyse cryoEM structure DrdV-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LVV
- Type
- protein + DNA
- Length
- 2,422 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.25
- Source
- Deinococcus wulumuqiensis; SYNTHETIC CONSTRUCT
- Molecule
- Site-specific DNA-methyltransferase (adenine-specific); DNA (28-mer); DNA (27-mer)
- EC
- 2.1.1.72
- UniProt
- A0A345IJ72
- Ligands
- SAM, CA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 3.25 · 6 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 1011 | 41% helix, 11% strand | A0A345IJ72 |
| B | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 1012 | 43% helix, 13% strand | A0A345IJ72 |
| C | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 143 | 39% helix, 24% strand | A0A345IJ72 |
| D | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 146 | 39% helix, 18% strand | A0A345IJ72 |
| E, G | DNA (28-mer) | dna | 28 | — | — |
| F, H | DNA (27-mer) | dna | 27 | — | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, E, B, G
- CA · Calcium ion · metal · 4 copies · chains A, G, B, E, C, F, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1098 | 0.86 | 0.87 | 98 | empty |
| 2 | 1194 | 0.84 | 0.85 | 119 | empty |
| 3 | 251 | 0.83 | 0.96 | 28 | empty |
| 4 | 871 | 0.83 | 0.85 | 96 | empty |
| 5 | 208 | 0.81 | 0.96 | 29 | empty |
Interfaces
19 interfaces between chains.
- B–G · 1431 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–F · 1412 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–H · 1313 Ų buried · 30 hydrogen bonds · protein-nucleic
- G–H · 1306 Ų buried · 153 hydrogen bonds · nucleic-nucleic
- A–E · 1306 Ų buried · 26 hydrogen bonds · protein-nucleic
Compared structures
- 7LVV · Cryoem structure drdv-DNA complex · the same entry in another collection · chain A against A, 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 A0A345IJ72
- Elsewhere: RCSB PDB 7LVV · PDBe 7LVV · UniProt A0A345IJ72
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