Research workbench
Structure of the complex of monomeric sarcosine with its substrate analogue inhibitor 2-furoic acid at 1.3 a resolution.
Analyse Structure of the complex of monomeric sarcosine with its substrate analogue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GF3
- Type
- protein
- Length
- 770 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monomeric sarcosine oxidase
- EC
- 1.5.3.1
- UniProt
- P40859
- Ligands
- FOA, FAD, PO4, CL
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Monomeric sarcosine oxidase (EC 1.5.3.1) | protein | 385 | 32% helix, 31% strand | P40859 |
Ligands and binding sites
- FOA · 2-furoic acid · ligand · 4 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.86 | 0.96 | 58 | CL, FAD, FOA |
| 2 | 349 | 0.86 | 0.95 | 59 | CL, FAD, FOA |
| 3 | 1124 | 0.82 | 0.83 | 93 | FOA |
Interfaces
1 interface between chains.
- A–B · 532 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 2GF3 · Structure of the complex of monomeric sarcosine with its substrate analogue inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P40859 · AlphaFold monomer V2.0 prediction for monomeric sarcosine oxidase (P40859) · 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 P40859
- Elsewhere: RCSB PDB 2GF3 · PDBe 2GF3 · UniProt P40859
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