MolNFT v1 · #34743 · protein
Dpnm DNA adenine methyltransferase from streptoccocus pneumoniae complexed with S-adenosylmethionine
2DPM · Protein (adenine-specific methyltransferase dpnii 1): “Dpnm DNA adenine methyltransferase from streptoccocus pneumoniae complexed with S-adenosylmethionine”. X-ray diffraction, 2 ligands (SAM, HG), 2 pockets (best druggability…
- PDB
- 2DPM
- Type
- protein
- Length
- 258 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (adenine-specific methyltransferase dpnii 1)
- EC
- 2.1.1.72
- UniProt
- P04043
- Ligands
- SAM, HG
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (adenine-specific methyltransferase dpnii 1) (EC 2.1.1.72) | protein | 258 | 44% helix, 16% strand | P04043 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.63 | 0.77 | 46 | SAM |
| 2 | 57 | 0.30 | 0.75 | 17 | empty |
Compared structures
- 2DPM · Dpnm DNA adenine methyltransferase from streptoccocus pneumoniae complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P04043 · AlphaFold monomer V2.0 prediction for modification methylase dpniia (P04043) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P04043
- Elsewhere: RCSB PDB 2DPM · PDBe 2DPM · UniProt P04043
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