Research workbench
Crystal structure of rat glycine N-methyltransferase apoprotein, monoclinic form
Analyse Crystal structure of rat glycine N-methyltransferase apoprotein, monoclinic form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IDJ
- Type
- protein
- Length
- 1,129 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine N-methyltransferase
- EC
- 2.1.1.20
- UniProt
- P13255
- Ligands
- CA
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 277 | 31% helix, 29% strand | P13255 |
| B | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 285 | 31% helix, 28% strand | P13255 |
| C | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 280 | 31% helix, 28% strand | P13255 |
| D | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 287 | 30% helix, 30% strand | P13255 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.82 | 0.93 | 51 | empty |
| 2 | 171 | 0.79 | 0.95 | 36 | CA |
| 3 | 261 | 0.79 | 0.91 | 49 | empty |
| 4 | 346 | 0.76 | 0.87 | 48 | empty |
| 5 | 345 | 0.76 | 0.87 | 45 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2323 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2308 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1026 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 864 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 105 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2IDJ · Crystal Structure of Rat Glycine N-Methyltransferase Apoprotein, Monoclinic Form · the same entry in another collection · chain D against D, TM-score 1.00
- P13255 · AlphaFold monomer V2.0 prediction for glycine N-methyltransferase (P13255) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P13255
- Elsewhere: RCSB PDB 2IDJ · PDBe 2IDJ · UniProt P13255
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