Research workbench
Role of histidine 269 in catalysis by monomeric sarcosine oxidase
Analyse Role of histidine 269 in catalysis by monomeric sarcosine oxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L9D
- 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, PYC, CL
- Pockets
- 2 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Monomeric sarcosine oxidase (EC 1.5.3.1) | protein | 385 | 32% helix, 30% strand | P40859 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- PYC · Pyrrole-2-carboxylate · 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
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 | 404 | 0.84 | 0.92 | 68 | CL, FAD, PYC |
| 2 | 421 | 0.84 | 0.91 | 67 | CL, FAD, PYC |
Interfaces
1 interface between chains.
- A–B · 46 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 1L9D · Role of Histidine 269 in Catalysis by Monomeric Sarcosine Oxidase · 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 1L9D · PDBe 1L9D · UniProt P40859
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