Research workbench
Crystal structure of trans-aconitate methyltransferase from agrobacterium tumefaciens
Analyse Crystal structure of trans-aconitate methyltransferase from agrobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P35
- Type
- protein
- Length
- 485 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trans-aconitate 2-methyltransferase
- EC
- 2.1.1.144
- UniProt
- Q8UH15
- Ligands
- SAH
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trans-aconitate 2-methyltransferase (EC 2.1.1.144) | protein | 245 | 42% helix, 25% strand | Q8UH15 |
| B | Trans-aconitate 2-methyltransferase (EC 2.1.1.144) | protein | 240 | 45% helix, 26% strand | Q8UH15 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
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 | 929 | 0.74 | 0.78 | 101 | SAH |
| 2 | 446 | 0.62 | 0.76 | 54 | SAH |
| 3 | 90 | 0.34 | 0.74 | 21 | empty |
| 4 | 65 | 0.29 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1383 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2P35 · Crystal structure of trans-aconitate methyltransferase from Agrobacterium tumefaciens · the same entry in another collection · chain B against B, TM-score 1.00
- Q8UH15 · AlphaFold monomer V2.0 prediction for trans-aconitate 2-methyltransferase (Q8UH15) · 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 Q8UH15
- Elsewhere: RCSB PDB 2P35 · PDBe 2P35 · UniProt Q8UH15
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