MolNFT v1 · #5544 · protein
Complex of monomeric sarcosine oxidase with the inhibitor [METHYLSELENO]CETATE
1EL8: “Complex of monomeric sarcosine oxidase with the inhibitor [METHYLSELENO]CETATE”. X-ray diffraction, 4 ligands (FAD, MSF, PO4), 3 pockets (best druggability 0.86). MolNFT v1 #5544 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1EL8
- Type
- protein
- Length
- 770 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sarcosine oxidase
- EC
- 1.5.3.1
- UniProt
- P40859
- Ligands
- FAD, MSF, 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 | Sarcosine oxidase (EC 1.5.3.1) | protein | 385 | 32% helix, 31% strand | P40859 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MSF · [methylseleno]acetate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · 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 | 332 | 0.86 | 0.95 | 57 | CL, FAD, MSF |
| 2 | 319 | 0.85 | 0.95 | 58 | CL, FAD, MSF |
| 3 | 1134 | 0.82 | 0.83 | 97 | empty |
Interfaces
1 interface between chains.
- A–B · 486 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 1EL8 · Complex of monomeric sarcosine oxidase with the inhibitor [METHYLSELENO]CETATE · 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 1EL8 · PDBe 1EL8 · UniProt P40859
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