MolNFT v1 · #56153 · protein + DNA
S-adenosyl-L-methionine-dependent methyl transfer: observable precatalytic intermediates during DNA cytosine methylation
2Z6A · DNA (5'-D(*DGP*DAP*DTP*DAP*DGP*DCP*DGP*DCP*DTP*DAP*DTP*DC)…: “S-adenosyl-L-methionine-dependent methyl transfer: observable precatalytic intermediates during DNA cytosine…”. X-ray diffraction, 1 ligand (SAH), 5 pockets (best…
- PDB
- 2Z6A
- Type
- protein + DNA
- Length
- 352 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*DGP*DAP*DTP*DAP*DGP*DCP*DGP*DCP*DTP*DAP*DTP*DC)- 3'); DNA (5'…
- EC
- 2.1.1.37
- UniProt
- P05102
- Ligands
- SAH
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(*DGP*DAP*DTP*DAP*DGP*DCP*DGP*DCP*DTP*DAP*DTP*DC)- 3') | dna | 12 | — | — |
| D | DNA (5'- D(*DTP*DGP*DAP*DTP*DAP*DGP*DCP*DGP*DCP*DTP*DAP*DTP*DC)-3') | dna | 13 | — | — |
| A | Modification methylase hhai (EC 2.1.1.37) | protein | 327 | 32% helix, 19% strand | P05102 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.73 | 0.88 | 35 | SAH |
| 2 | 148 | 0.52 | 0.80 | 18 | empty |
| 3 | 54 | 0.36 | 0.79 | 17 | empty |
| 4 | 93 | 0.36 | 0.75 | 14 | empty |
| 5 | 81 | 0.32 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- D–A · 1021 Ų buried · 36 hydrogen bonds · protein-nucleic
- C–A · 697 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 541 Ų buried · 42 hydrogen bonds · nucleic-nucleic
Compared structures
- 2Z6A · S-Adenosyl-L-methionine-Dependent Methyl Transfer: Observable Precatalytic Intermediates… · the same entry in another collection · chain A against A, TM-score 1.00
- P05102 · AlphaFold monomer V2.0 prediction for modification methylase hhai (P05102) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P05102
- Elsewhere: RCSB PDB 2Z6A · PDBe 2Z6A · UniProt P05102
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