MolNFT v1 · #62410 · protein + DNA
M. hhai co-crystallized with synthetic dsdna containing a propane diol in place of the deoxycytidine residue targeted for methylation.
3EEO · 5'- D(P*DCP*DCP*DAP*DTP*DGP*DCP*DGP*DCP*DTP*DGP*DAP*DC)-3': “M. hhai co-crystallized with synthetic dsdna containing a propane diol in place of the deoxycytidine residue…”. X-ray diffraction, 2 ligands (PDI, SAM), 4 pockets (best…
- PDB
- 3EEO
- Type
- protein + DNA
- Length
- 350 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(P*DCP*DCP*DAP*DTP*DGP*DCP*DGP*DCP*DTP*DGP*DAP*DC)-3'…
- EC
- 2.1.1.37
- UniProt
- P05102
- Ligands
- PDI, SAM
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'- D(P*DCP*DCP*DAP*DTP*DGP*DCP*DGP*DCP*DTP*DGP*DAP*DC)-3' | dna | 12 | — | — |
| D | 5'-D(P*DGP*DTP*DCP*DAP*DGP*(PDI) P*DGP*DCP*DAP*DTP*DGP*DG)-3' | dna | 11 | — | — |
| A | Modification methylase hhai (EC 2.1.1.37) | protein | 327 | 34% helix, 19% strand | P05102 |
Ligands and binding sites
- PDI · Phosphoric acid mono-(3-hydroxy-propyl) ester · ligand · chains D, A
- SAM · S-adenosylmethionine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.80 | 0.90 | 65 | PDI, SAM |
| 2 | 213 | 0.59 | 0.81 | 24 | empty |
| 3 | 179 | 0.53 | 0.79 | 25 | empty |
| 4 | 68 | 0.32 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- D–A · 824 Ų buried · 21 hydrogen bonds · protein-nucleic
- C–A · 708 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 564 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3EEO · M. HhaI co-crystallized with synthetic dsDNA containing a propane diol in place of the… · 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 3EEO · PDBe 3EEO · UniProt P05102
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