Research workbench
Hhai DNA methyltransferase R163N mutant complex with 13MER gcgc-gmgc oligonucleotide and sah
Analyse Hhai DNA methyltransferase R163N mutant complex with 13MER gcgc-gmgc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2UYC
- Type
- protein + DNA
- Length
- 352 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Modification methylase hhai; 5'-D(*TP*GP*GP*AP*TP*GP*5CMP*GP*CP*TP *GP*AP*C)-3'…
- EC
- 2.1.1.37
- UniProt
- P05102
- Ligands
- SAH, SO4
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Modification methylase hhai (EC 2.1.1.37) | protein | 327 | 32% helix, 19% strand | P05102 |
| C | 5'-D(*TP*GP*GP*AP*TP*GP*5CMP*GP*CP*TP *GP*AP*C)-3' | dna | 13 | — | — |
| D | 5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP *CP*C)-3' | dna | 12 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, D
- SO4 · Sulfate ion · ion · 6 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.77 | 0.86 | 52 | SAH, GOL |
| 2 | 167 | 0.55 | 0.81 | 23 | empty |
| 3 | 58 | 0.31 | 0.77 | 14 | empty |
| 4 | 53 | 0.26 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–D · 982 Ų buried · 33 hydrogen bonds · protein-nucleic
- A–C · 853 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–D · 527 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2UYC · HhaI DNA methyltransferase R163N mutant complex with 13mer GCGC-GMGC oligonucleotide and… · 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 2UYC · PDBe 2UYC · UniProt P05102
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