Research workbench
Structure of the N-acetyl-D-glucosamine oxidase from ralstonia solanacearum
Analyse Structure of the N-acetyl-D-glucosamine oxidase from ralstonia solanacearum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZZK
- Type
- protein
- Length
- 975 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetyl-D-hexosamine oxidase
- EC
- 1.1.3.29
- UniProt
- A3RXB7
- Ligands
- FAD, ALA
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetyl-D-hexosamine oxidase (EC 1.1.3.29) | protein | 486 | 33% helix, 22% strand | A3RXB7 |
| B | N-acetyl-D-hexosamine oxidase (EC 1.1.3.29) | protein | 489 | 32% helix, 22% strand | A3RXB7 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- ALA · Alanine · ligand · chains A
- GOL · Glycerol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.83 | 0.86 | 103 | FAD, PEG, GOL |
| 2 | 774 | 0.82 | 0.85 | 102 | FAD |
| 3 | 125 | 0.79 | 0.97 | 21 | PEG |
| 4 | 123 | 0.79 | 0.97 | 22 | empty |
| 5 | 185 | 0.62 | 0.84 | 39 | PEG |
Interfaces
1 interface between chains.
- A–B · 1698 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 2 disulfide, 1 covalent (flavinylation, disulfide, covalent ligand).
Compared structures
- 7ZZK · Structure of the N-acetyl-D-glucosamine oxidase from Ralstonia Solanacearum · the same entry in another collection · chain A 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 A3RXB7
- Elsewhere: RCSB PDB 7ZZK · PDBe 7ZZK · UniProt A3RXB7
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