MolNFT v1 · #56168 · protein + DNA
Ternary structure of ARG165ALA M.HHAI C5-cytosine DNA methyltransferase with unmodified DNA and adohcy
2Z6Q · DNA (5'-D(*DGP*DAP*DTP*DAP*DGP*DCP*DGP*DCP*DTP*DAP*DTP*DC)…: “Ternary structure of ARG165ALA M.HHAI C5-cytosine DNA methyltransferase with unmodified DNA and adohcy”. X-ray diffraction, 2 ligands (DCZ, SAH), 2 pockets (best…
- PDB
- 2Z6Q
- Type
- protein + DNA
- Length
- 351 residues
- Chains
- 4
- 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…
- EC
- 2.1.1.37
- UniProt
- P05102
- Ligands
- DCZ, SAH
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 18% 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*DG)-3') | dna | 6 | — | — |
| E | DNA (5'-D(*DGP*DCP*DTP*DAP*DTP*DC)-3') | dna | 6 | — | — |
| A | Modification methylase hhai (EC 2.1.1.37) | protein | 327 | 30% helix, 18% strand | P05102 |
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 | 623 | 0.79 | 0.85 | 74 | DCZ, SAH |
| 2 | 51 | 0.28 | 0.76 | 11 | empty |
Interfaces
5 interfaces between chains.
- C–A · 697 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–A · 423 Ų buried · 12 hydrogen bonds · protein-nucleic
- E–A · 353 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–E · 279 Ų buried · 19 hydrogen bonds · nucleic-nucleic
- C–D · 242 Ų buried · 19 hydrogen bonds · nucleic-nucleic
Compared structures
- 2Z6Q · Ternary structure of Arg165Ala M.HhaI C5-Cytosine DNA methyltransferase with unmodified… · the same entry in another collection · chain C against C, 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 2Z6Q · PDBe 2Z6Q · UniProt P05102
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