Research workbench
Crystal structure of R49K mutant of monomeric sarcosine oxidase crystallized in phosphate as precipitant
Analyse Crystal structure of R49K mutant of monomeric sarcosine oxidase crystallized in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BHK
- 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
- FAD, 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
- FAD · Flavin-adenine dinucleotide · ligand · 2 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 | 332 | 0.86 | 0.96 | 54 | CL, FAD |
| 2 | 349 | 0.85 | 0.95 | 59 | CL, FAD |
| 3 | 1165 | 0.82 | 0.83 | 91 | empty |
Interfaces
1 interface between chains.
- A–B · 506 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 3BHK · Crystal structure of R49K mutant of monomeric sarcosine oxidase crystallized in phosphate… · 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 3BHK · PDBe 3BHK · UniProt P40859
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