MolNFT v1 · #11218 · protein
Crystal structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with adenosine & VYP(ISP)HA substrate
1JG3 · Protein-L-isoaspartate O-methyltransferase: “Crystal structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with adenosine & VYP(ISP)HA substrate”. X-ray diffraction, 3 ligands (ADN, NA, CL), 3 pockets (best druggability 0.78).…
- PDB
- 1JG3
- Type
- protein
- Length
- 442 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-L-isoaspartate O-methyltransferase; VYP(L-iso-ASP)HA
- EC
- 2.1.1.77
- UniProt
- Q8TZR3
- Ligands
- ADN, NA, CL
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein-L-isoaspartate O-methyltransferase (EC 2.1.1.77) | protein | 215 | 39% helix, 27% strand | Q8TZR3 |
| C, D | VYP(L-iso-ASP)HA | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- ADN · Adenosine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, C, B, D
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.78 | 0.95 | 36 | NA, ADN |
| 2 | 124 | 0.77 | 0.96 | 36 | NA, ADN |
| 3 | 192 | 0.48 | 0.75 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 478 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 468 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 356 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 1JG3 · Crystal Structure of L-isoaspartyl (D-aspartyl) O-methyltransferase with adenosine &… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TZR3 · AlphaFold monomer V2.0 prediction for protein-L-isoaspartate O-methyltransferase (Q8TZR3) · a predicted model of the same protein · chain A 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 Q8TZR3
- Elsewhere: RCSB PDB 1JG3 · PDBe 1JG3 · UniProt Q8TZR3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.