MolNFT v1 · #181213 · protein + DNA
Cryoem structure drdv-DNA complex
7LO5 · Site-specific DNA-methyltransferase (adenine-specific): “Cryoem structure drdv-DNA complex”. Electron microscopy, 2 ligands (SAM, CA), 20 pockets (best druggability 0.86). MolNFT v1 #181213 on GenesisL1: 3D structure, binding sites…
- PDB
- 7LO5
- Type
- protein + DNA
- Length
- 4,270 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 8 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 1016 | 46% helix, 15% strand | A0A345IJ72 |
| B | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 1013 | 45% helix, 15% strand | A0A345IJ72 |
| C | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 1014 | 45% helix, 14% strand | A0A345IJ72 |
| D | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 1012 | 43% helix, 14% strand | A0A345IJ72 |
| E, G, I | DNA (28-mer) | dna | 28 | — | — |
| F, H, J | DNA (27-mer) | dna | 27 | — | — |
| K | DNA (28-mer) | dna | 25 | — | — |
| L | DNA (27-mer) | dna | 25 | — | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, E, B, G, C, I, D, K
- 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 | 944 | 0.86 | 0.88 | 94 | empty |
| 2 | 1154 | 0.85 | 0.86 | 126 | empty |
| 3 | 833 | 0.85 | 0.88 | 103 | empty |
| 4 | 944 | 0.82 | 0.84 | 104 | empty |
| 5 | 1074 | 0.82 | 0.83 | 113 | empty |
Interfaces
25 interfaces between chains.
- A–D · 1698 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1670 Ų buried · 31 hydrogen bonds · protein-protein
- I–J · 1500 Ų buried · 152 hydrogen bonds · nucleic-nucleic
- C–J · 1470 Ų buried · 33 hydrogen bonds · protein-nucleic
- B–G · 1441 Ų buried · 22 hydrogen bonds · protein-nucleic
Compared structures
- 7LO5 · cryoEM structure DrdV-DNA complex · the same entry in another collection · chain F against F, 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 7LO5 · PDBe 7LO5 · UniProt A0A345IJ72
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