MolNFT v1 · #4346 · protein
Protein-L-isoaspartate O-methyltransferase
1DL5: “Protein-L-isoaspartate O-methyltransferase”. X-ray diffraction, 3 ligands (SAH, CD, CL), 5 pockets (best druggability 0.69). MolNFT v1 #4346 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1DL5
- Type
- protein
- Length
- 633 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
- Q56308
- Ligands
- SAH, CD, CL
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-L-isoaspartate O-methyltransferase (EC 2.1.1.77) | protein | 317 | 35% helix, 31% strand | Q56308 |
| B | Protein-L-isoaspartate O-methyltransferase (EC 2.1.1.77) | protein | 316 | 34% helix, 31% strand | Q56308 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 9 copies · chains B, A
- CL · Chloride ion · ion · 10 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.69 | 0.87 | 38 | SAH |
| 2 | 215 | 0.68 | 0.85 | 45 | SAH |
| 3 | 207 | 0.56 | 0.79 | 30 | empty |
| 4 | 224 | 0.55 | 0.78 | 29 | empty |
| 5 | 76 | 0.37 | 0.77 | 18 | CD, CL |
Interfaces
1 interface between chains.
- A–B · 563 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 Q56308
- Elsewhere: RCSB PDB 1DL5 · PDBe 1DL5 · UniProt Q56308
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