Research workbench
Hhai methyltransferase in complex with DNA containing an abasic south carbocyclic sugar at its target site
Analyse Hhai methyltransferase in complex with DNA containing an abasic south… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SKM
- Type
- protein + DNA
- Length
- 352 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3'…
- EC
- 2.1.1.37
- UniProt
- P05102
- Ligands
- SAH
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*TP*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3' | dna | 13 | — | — |
| D | 5'-D(*T*GP*TP*CP*AP*GP*(HCX)P*GP*CP*AP*TP*GP*G)- 3' | dna | 12 | — | — |
| A | Modification methylase hhai (EC 2.1.1.37) | protein | 327 | 33% helix, 18% strand | P05102 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.76 | 0.89 | 39 | SAH |
| 2 | 62 | 0.73 | 0.99 | 22 | empty |
| 3 | 221 | 0.59 | 0.81 | 25 | empty |
| 4 | 140 | 0.51 | 0.80 | 18 | empty |
| 5 | 66 | 0.30 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- D–A · 912 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–A · 825 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–D · 554 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1SKM · HhaI methyltransferase in complex with DNA containing an abasic south carbocyclic sugar… · 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 1SKM · PDBe 1SKM · UniProt P05102
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