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Cama adenine methyltransferase complexed to cognate substrate DNA and inhibitor sinefungin
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
- 7RFK
- Type
- protein + DNA
- Length
- 1,788 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
- SFG, K
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 568 | 43% helix, 19% strand | Q183J3 |
| B | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 575 | 41% helix, 19% strand | Q183J3 |
| C | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 562 | 42% helix, 18% strand | Q183J3 |
| E | DNA strand 2 | dna | 13 | — | — |
| D, F, H | DNA strand 1 | dna | 14 | — | — |
| G, I | DNA strand 2 | dna | 14 | — | — |
Ligands and binding sites
- SFG · Sinefungin · ligand · 3 copies · chains A, D, B, F, C, H
- K · Potassium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, E, B, C, H, F, I, G
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 | 728 | 0.72 | 0.79 | 59 | EDO |
| 2 | 569 | 0.69 | 0.79 | 51 | EDO |
| 3 | 167 | 0.68 | 0.88 | 36 | SFG, EDO |
| 4 | 176 | 0.68 | 0.87 | 34 | SFG, EDO |
| 5 | 559 | 0.67 | 0.78 | 58 | empty |
Interfaces
19 interfaces between chains.
- C–H · 1304 Ų buried · 36 hydrogen bonds · protein-nucleic
- B–F · 1301 Ų buried · 32 hydrogen bonds · protein-nucleic
- A–D · 1279 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–E · 1176 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–G · 1154 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 7RFK · CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Inhibitor Sinefungin · the same entry in another collection · chain C against C, 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 7RFK · PDBe 7RFK · UniProt Q183J3
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