MolNFT v1 · #76688 · protein
Crystal structure for the complex of substrate-reduced msox with sarcosine
3QSE · Monomeric sarcosine oxidase: “Crystal structure for the complex of substrate-reduced msox with sarcosine”. X-ray diffraction, 3 ligands (FAD, SAR, CL), 8 pockets (best druggability 0.85). MolNFT v1 #76688 on GenesisL1: 3D structure…
- PDB
- 3QSE
- Type
- protein
- Length
- 767 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
- FAD, SAR, CL
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Monomeric sarcosine oxidase (EC 1.5.3.1) | protein | 385 | 31% helix, 31% strand | P40859 |
| B | Monomeric sarcosine oxidase (EC 1.5.3.1) | protein | 382 | 32% helix, 31% strand | P40859 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- SAR · Sarcosine · ligand · 2 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
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.85 | 0.95 | 56 | CL, FAD, SAR |
| 2 | 346 | 0.85 | 0.94 | 61 | FAD, CL, SAR |
| 3 | 64 | 0.33 | 0.76 | 18 | empty |
| 4 | 68 | 0.32 | 0.75 | 18 | empty |
| 5 | 77 | 0.32 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1010 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 3QSE · Crystal structure for the complex of substrate-reduced msox with sarcosine · the same entry in another collection · chain B against B, TM-score 1.00
- P40859 · AlphaFold monomer V2.0 prediction for monomeric sarcosine oxidase (P40859) · a predicted model of the same protein · chain B 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 3QSE · PDBe 3QSE · UniProt P40859
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