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Cama adenine methyltransferase complexed to cognate substrate DNA and inhibitor SGC8158
Analyse Cama adenine methyltransferase complexed to cognate substrate DNA and inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RFN
- Type
- protein + DNA
- Length
- 1,717 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
- Ligands
- MJ7, K
- Pockets
- 20 · best druggability 0.69
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 | 545 | 40% helix, 20% strand | Q183J3 |
| B | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 550 | 40% helix, 20% strand | Q183J3 |
| C | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 538 | 42% helix, 20% strand | Q183J3 |
| E, G, I | DNA strand 2 | dna | 14 | — | — |
| D, F, H | DNA strand 1 | dna | 14 | — | — |
Ligands and binding sites
- MJ7 · 5'-S-(4-{[(4'-chloro[1,1'-biphenyl]-3-yl) methyl]amino}butyl)-5'-thioadenosine · ligand · 3 copies · chains A, D, B, F, C, H
- K · Potassium ion · metal · 7 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C, F, 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 | 1086 | 0.69 | 0.74 | 71 | EDO |
| 2 | 392 | 0.66 | 0.80 | 45 | empty |
| 3 | 349 | 0.66 | 0.81 | 48 | K |
| 4 | 390 | 0.65 | 0.79 | 40 | EDO, K |
| 5 | 298 | 0.64 | 0.81 | 41 | empty |
Interfaces
19 interfaces between chains.
- B–F · 1316 Ų buried · 30 hydrogen bonds · protein-nucleic
- C–H · 1313 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–D · 1306 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–G · 1117 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–E · 1075 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 7RFN · CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor SGC8158 · 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 7RFN · PDBe 7RFN · UniProt Q183J3
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