MolNFT v1 · #40031 · protein
Crystal structure of rat glycine N-methyltransferase complexed with folate
2IDK: “Crystal structure of rat glycine N-methyltransferase complexed with folate”. X-ray diffraction, 1 ligand (C2F), 14 pockets (best druggability 0.83). MolNFT v1 #40031 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2IDK
- Type
- protein
- Length
- 1,130 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
- C2F
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 277 | 31% helix, 27% 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 | 281 | 30% helix, 27% strand | P13255 |
| D | Glycine N-methyltransferase (EC 2.1.1.20) | protein | 287 | 30% helix, 30% strand | P13255 |
Ligands and binding sites
- C2F · 5-methyl-5,6,7,8-tetrahydrofolic acid · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.83 | 0.94 | 47 | empty |
| 2 | 329 | 0.81 | 0.91 | 44 | empty |
| 3 | 218 | 0.79 | 0.93 | 46 | empty |
| 4 | 208 | 0.78 | 0.92 | 46 | empty |
| 5 | 461 | 0.76 | 0.85 | 57 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2319 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2313 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 997 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 975 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 177 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2IDK · Crystal Structure of Rat Glycine N-Methyltransferase Complexed With Folate · 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 B 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 2IDK · PDBe 2IDK · UniProt P13255
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