Research workbench
Crystal structure of the SAM-dependent methyltransferase from pyrococcus horikoshii OT3
Analyse Crystal structure of the SAM-dependent methyltransferase from pyrococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WZN
- Type
- protein
- Length
- 732 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SAM-dependent methyltransferase
- EC
- 2.1.1.-
- Ligands
- SAH, MG, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | SAM-dependent methyltransferase (EC 2.1.1.-) | protein | 244 | 32% helix, 36% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.73 | 0.82 | 58 | SAH |
| 2 | 472 | 0.72 | 0.81 | 59 | SAH |
| 3 | 466 | 0.70 | 0.80 | 50 | SAH |
Interfaces
3 interfaces between chains.
- A–B · 615 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 614 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 603 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1WZN · Crystal Structure of the SAM-dependent methyltransferase from Pyrococcus horikoshii OT3 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1WZN · PDBe 1WZN
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