MolNFT v1 · #30740 · protein
Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme
2A89: “Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme”. X-ray diffraction, 3 ligands (FCG, CL, PO4), 2 pockets (best druggability 0.89). MolNFT v1 #30740 on GenesisL1: 3D structure, binding sites…
- PDB
- 2A89
- 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
- FCG, CL, PO4
- Pockets
- 2 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Monomeric sarcosine oxidase (EC 1.5.3.1) | protein | 385 | 31% helix, 32% strand | P40859 |
Ligands and binding sites
- FCG · (N5,C4A)-(alpha-hydroxy-propano)-3,4,4A,5-tetrahydro-flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.89 | 0.90 | 145 | CL, FCG |
| 2 | 339 | 0.86 | 0.96 | 59 | CL, FCG |
Interfaces
1 interface between chains.
- A–B · 605 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2A89 · Monomeric Sarcosine Oxidase: Structure of a covalently flavinylated amine oxidizing enzyme · 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 2A89 · PDBe 2A89 · UniProt P40859
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