MolNFT v1 · #29963 · protein
Crystal structure of monomeric sarcosine oxidase from bacillus sp. ns- 129
1ZOV: “Crystal structure of monomeric sarcosine oxidase from bacillus sp. ns- 129”. X-ray diffraction, 2 ligands (FAD, CL), 6 pockets (best druggability 0.84). MolNFT v1 #29963 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1ZOV
- Type
- protein
- Length
- 761 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
- P23342
- Ligands
- FAD, CL
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Monomeric sarcosine oxidase (EC 1.5.3.1) | protein | 381 | 31% helix, 29% strand | P23342 |
| B | Monomeric sarcosine oxidase (EC 1.5.3.1) | protein | 380 | 32% helix, 29% strand | P23342 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · 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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.84 | 0.94 | 54 | CL, FAD |
| 2 | 414 | 0.83 | 0.91 | 67 | CL, FAD |
| 3 | 98 | 0.37 | 0.75 | 17 | empty |
| 4 | 71 | 0.33 | 0.75 | 20 | empty |
| 5 | 63 | 0.31 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 979 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 1ZOV · Crystal Structure of Monomeric Sarcosine Oxidase from Bacillus sp. NS-129 · the same entry in another collection · chain A against A, TM-score 1.00
- P23342 · AlphaFold monomer V2.0 prediction for monomeric sarcosine oxidase (P23342) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P23342
- Elsewhere: RCSB PDB 1ZOV · PDBe 1ZOV · UniProt P23342
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