Research workbench
Crystal structure of putative methyltransferase from pseudomonas syringae pv. tomato
Analyse Crystal structure of putative methyltransferase from pseudomonas syringae pv.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P7C
- Type
- protein
- Length
- 641 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (MO5U34)-methyltransferase
- EC
- 2.1.1.-
- UniProt
- Q87XG5
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (MO5U34)-methyltransferase (EC 2.1.1.-) | protein | 322 | 33% helix, 26% strand | Q87XG5 |
| B | TRNA (MO5U34)-methyltransferase (EC 2.1.1.-) | protein | 319 | 34% helix, 26% strand | Q87XG5 |
Ligands and binding sites
- ACT · Acetate ion · additive · 3 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.81 | 0.82 | 121 | ACT |
| 2 | 369 | 0.68 | 0.81 | 39 | ACT |
| 3 | 100 | 0.36 | 0.74 | 20 | empty |
| 4 | 68 | 0.28 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 609 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4P7C · Crystal structure of putative methyltransferase from Pseudomonas syringae pv. tomato · the same entry in another collection · chain A against A, TM-score 1.00
- Q87XG5 · AlphaFold monomer V2.0 prediction for tRNA U34 carboxymethyltransferase (Q87XG5) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q87XG5
- Elsewhere: RCSB PDB 4P7C · PDBe 4P7C · UniProt Q87XG5
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