Research workbench
Crystal structure of methanocaldococcus jannaschii TRM5 in complex with adenosine
Analyse Crystal structure of methanocaldococcus jannaschii TRM5 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AY0
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein MJ0883
- UniProt
- Q58293
- Ligands
- ADN, ZN
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein MJ0883 | protein | 320 | 28% helix, 33% strand | Q58293 |
| B | Uncharacterized protein MJ0883 | protein | 314 | 26% helix, 30% strand | Q58293 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.77 | 0.79 | 82 | ZN, ADN |
| 2 | 193 | 0.71 | 0.87 | 20 | empty |
| 3 | 426 | 0.65 | 0.78 | 47 | ADN |
| 4 | 59 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 211 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3AY0 · Crystal structure of Methanocaldococcus jannaschii Trm5 in complex with adenosine · the same entry in another collection · chain A against A, TM-score 1.00
- Q58293 · AlphaFold monomer V2.0 prediction for tRNA (GUANINE(37)-N1)-methyltransferase TRM5B… · a predicted model of the same protein · chain B against A, TM-score 0.79
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 Q58293
- Elsewhere: RCSB PDB 3AY0 · PDBe 3AY0 · UniProt Q58293
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