MolNFT v1 · #55862 · protein
Crystal structure of L-isoaspartyl protein carboxyl methyltranferase
2YXE · Protein-L-isoaspartate O-methyltransferase: “Crystal structure of L-isoaspartyl protein carboxyl methyltranferase”. X-ray diffraction, 5 pockets (best druggability 0.72). MolNFT v1 #55862 on GenesisL1: 3D structure, binding sites…
- PDB
- 2YXE
- Type
- protein
- Length
- 427 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-L-isoaspartate O-methyltransferase
- EC
- 2.1.1.77
- UniProt
- Q57636
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-L-isoaspartate O-methyltransferase (EC 2.1.1.77) | protein | 214 | 37% helix, 30% strand | Q57636 |
| B | Protein-L-isoaspartate O-methyltransferase (EC 2.1.1.77) | protein | 213 | 36% helix, 30% strand | Q57636 |
Ligands and binding sites
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.72 | 0.85 | 37 | empty |
| 2 | 195 | 0.71 | 0.88 | 34 | empty |
| 3 | 83 | 0.70 | 0.94 | 27 | empty |
| 4 | 69 | 0.34 | 0.76 | 13 | empty |
| 5 | 95 | 0.33 | 0.73 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 951 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2YXE · Crystal structure of L-isoaspartyl protein carboxyl methyltranferase · the same entry in another collection · chain A against A, TM-score 1.00
- Q57636 · AlphaFold monomer V2.0 prediction for protein-L-isoaspartate O-methyltransferase (Q57636) · 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 Q57636
- Elsewhere: RCSB PDB 2YXE · PDBe 2YXE · UniProt Q57636
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