MolNFT v1 · #181193 · protein + DNA
Semet cama adenine methyltransferase complexed to cognate substrate DNA
7LNI · Site-specific DNA-methyltransferase (adenine-specific): “Semet cama adenine methyltransferase complexed to cognate substrate DNA”. X-ray diffraction, 20 pockets (best druggability 0.68). MolNFT v1 #181193 on GenesisL1: 3D structure…
- PDB
- 7LNI
- Type
- protein + DNA
- Length
- 1,722 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Site-specific DNA-methyltransferase (adenine-specific); DNA strand 2; DNA strand 1
- EC
- 2.1.1.72
- UniProt
- Q183J3
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 547 | 40% helix, 20% strand | Q183J3 |
| B | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 551 | 40% helix, 20% strand | Q183J3 |
| C | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 540 | 39% helix, 20% strand | Q183J3 |
| E, G, I | DNA strand 2 | dna | 14 | — | — |
| D, F, H | DNA strand 1 | dna | 14 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, F, C, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.68 | 0.74 | 80 | EDO |
| 2 | 431 | 0.68 | 0.80 | 46 | empty |
| 3 | 378 | 0.66 | 0.80 | 49 | empty |
| 4 | 380 | 0.64 | 0.79 | 46 | empty |
| 5 | 307 | 0.63 | 0.80 | 42 | empty |
Interfaces
18 interfaces between chains.
- B–F · 1317 Ų buried · 29 hydrogen bonds · protein-nucleic
- C–H · 1307 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–D · 1295 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–E · 1155 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–G · 1128 Ų buried · 19 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 7LNI · SeMet CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA · the same entry in another collection · chain I against I, 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 Q183J3
- Elsewhere: RCSB PDB 7LNI · PDBe 7LNI · UniProt Q183J3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.