Research workbench
Crystal structure of the complex between adenosine and methanocaldococcus jannaschi DIM1
Analyse Crystal structure of the complex between adenosine and methanocaldococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GRV
- Type
- protein
- Length
- 262 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dimethyladenosine transferase
- EC
- 2.1.1.-
- UniProt
- Q58435
- Ligands
- ADN, SO4
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dimethyladenosine transferase (EC 2.1.1.-) | protein | 262 | 49% helix, 19% strand | Q58435 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.65 | 0.84 | 38 | ADN |
| 2 | 60 | 0.31 | 0.75 | 10 | empty |
Compared structures
- 3GRV · Crystal Structure of the Complex between Adenosine and Methanocaldococcus jannaschi Dim1 · 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 1.00
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 3GRV · PDBe 3GRV · UniProt Q58435
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