Research workbench
Oxidized L-alpha-glycerophosphate oxidase from mycoplasma pneumoniae with FAD bound
Analyse Oxidized L-alpha-glycerophosphate oxidase from mycoplasma pneumoniae with FAD… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X9M
- Type
- protein
- Length
- 384 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-alpha-glycerophosphate oxidase
- UniProt
- P75063
- Ligands
- FAD, G3P, NI
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-alpha-glycerophosphate oxidase | protein | 384 | 30% helix, 29% strand | P75063 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- G3P · Sn-glycerol-3-phosphate · ligand · chains A
- NI · Nickel (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.82 | 0.93 | 56 | FAD, G3P |
| 2 | 78 | 0.66 | 0.92 | 25 | empty |
| 3 | 178 | 0.58 | 0.81 | 25 | empty |
| 4 | 76 | 0.39 | 0.78 | 17 | empty |
| 5 | 51 | 0.32 | 0.77 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4X9M · Oxidized L-alpha-Glycerophosphate Oxidase from Mycoplasma pneumoniae with FAD bound · the same entry in another collection · chain A against A, TM-score 1.00
- P75063 · AlphaFold monomer V2.0 prediction for uncharacterized protein MG039 homolog (P75063) · 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 P75063
- Elsewhere: RCSB PDB 4X9M · PDBe 4X9M · UniProt P75063
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