Research workbench
Crystal structure of the conserved hypothetical protein, methyltransferase from streptococcus pneumoniae TIGR4
Analyse Crystal structure of the conserved hypothetical protein, methyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YZH
- Type
- protein
- Length
- 410 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (guanine-N(7)-)-methyltransferase
- EC
- 2.1.1.33
- UniProt
- P67506
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33) | protein | 204 | 40% helix, 20% strand | P67506 |
| B | TRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33) | protein | 206 | 37% helix, 20% strand | P67506 |
Ligands and binding sites
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.74 | 0.77 | 85 | empty |
| 2 | 276 | 0.58 | 0.78 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 384 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 1YZH · Crystal Structure of the Conserved Hypothetical Protein, Methyltransferase from… · the same entry in another collection · chain A against A, TM-score 1.00
- P67506 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(7)-)-methyltransferase (P67506) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P67506
- Elsewhere: RCSB PDB 1YZH · PDBe 1YZH · UniProt P67506
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