MolNFT v1 · #123238 · protein
Crystal structure of human L-ARGININE:GLYCINE amidinotransferase in complex with glycine
5JDW · Protein (L-ARGININE:GLYCINE amidinotransferase): “Crystal structure of human L-ARGININE:GLYCINE amidinotransferase in complex with glycine”. X-ray diffraction, 1 ligand (GLY), 3 pockets (best druggability 0.51). MolNFT v1 #123238 on…
- PDB
- 5JDW
- Type
- protein
- Length
- 360 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (L-ARGININE:GLYCINE amidinotransferase)
- EC
- 2.1.4.1
- UniProt
- P50440
- Ligands
- GLY
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (L-ARGININE:GLYCINE amidinotransferase) (EC 2.1.4.1) | protein | 360 | 29% helix, 23% strand | P50440 |
Ligands and binding sites
- GLY · Glycine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.51 | 0.86 | 25 | GLY |
| 2 | 86 | 0.38 | 0.76 | 13 | empty |
| 3 | 54 | 0.32 | 0.77 | 16 | empty |
Compared structures
- 5JDW · Crystal structure of human L-ARGININE:GLYCINE amidinotransferase in complex with glycine · the same entry in another collection · chain A against A, TM-score 1.00
- P50440 · AlphaFold monomer V2.0 prediction for glycine amidinotransferase, mitochondrial (P50440) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P50440
- Elsewhere: RCSB PDB 5JDW · PDBe 5JDW · UniProt P50440
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