Research workbench
Crystal structure of DIM1 from the thermophilic archeon, methanocaldococcus jannaschi
Analyse Crystal structure of DIM1 from the thermophilic archeon, methanocaldococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FYC
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable dimethyladenosine transferase
- EC
- 2.1.1.-
- UniProt
- Q58435
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable dimethyladenosine transferase (EC 2.1.1.-) | protein | 265 | 48% helix, 19% strand | Q58435 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.69 | 0.84 | 41 | empty |
| 2 | 412 | 0.65 | 0.79 | 49 | empty |
| 3 | 84 | 0.39 | 0.77 | 20 | empty |
| 4 | 78 | 0.36 | 0.77 | 15 | empty |
| 5 | 50 | 0.27 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 212 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3FYC · Crystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi · the same entry in another collection · chain A against A, TM-score 1.00
- Q58435 · AlphaFold monomer V2.0 prediction for probable ribosomal RNA small subunit… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q58435
- Elsewhere: RCSB PDB 3FYC · PDBe 3FYC · UniProt Q58435
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