Research workbench
Cama adenine methyltransferase complexed to cognate substrate DNA and cofactor sah
Analyse Cama adenine methyltransferase complexed to cognate substrate DNA and cofactor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LT5
- Type
- protein + DNA
- Length
- 1,787 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
- SAH
- Pockets
- 20 · best druggability 0.71
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 | 42% helix, 19% strand | Q183J3 |
| B | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 576 | 41% helix, 19% strand | Q183J3 |
| C | Site-specific DNA-methyltransferase (adenine-specific) (EC 2.1.1.72) | protein | 560 | 43% helix, 19% 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
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, D, B, F, C, H
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D, G, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.71 | 0.78 | 60 | EDO |
| 2 | 1144 | 0.70 | 0.74 | 73 | EDO |
| 3 | 154 | 0.69 | 0.88 | 36 | SAH, EDO |
| 4 | 542 | 0.68 | 0.78 | 56 | empty |
| 5 | 160 | 0.68 | 0.88 | 35 | SAH, EDO |
Interfaces
19 interfaces between chains.
- C–H · 1306 Ų buried · 33 hydrogen bonds · protein-nucleic
- B–F · 1303 Ų buried · 32 hydrogen bonds · protein-nucleic
- A–D · 1275 Ų buried · 31 hydrogen bonds · protein-nucleic
- B–G · 1141 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–I · 1130 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 7LT5 · CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Cofactor SAH · 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 Q183J3
- Elsewhere: RCSB PDB 7LT5 · PDBe 7LT5 · UniProt Q183J3
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