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Crystal structure of dodecameric FMN-dependent ubix-like decarboxylase from escherichia COLI O157:H7
Analyse Crystal structure of dodecameric FMN-dependent ubix-like decarboxylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SBZ
- Type
- protein
- Length
- 720 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable aromatic acid decarboxylase
- EC
- 4.1.1.-
- UniProt
- P69774
- Ligands
- FMN
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable aromatic acid decarboxylase (EC 4.1.1.-) | protein | 183 | 43% helix, 17% strand | P69774 |
| B, C | Probable aromatic acid decarboxylase (EC 4.1.1.-) | protein | 176 | 43% helix, 18% strand | P69774 |
| D | Probable aromatic acid decarboxylase (EC 4.1.1.-) | protein | 185 | 42% helix, 17% strand | P69774 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.73 | 0.84 | 46 | FMN |
| 2 | 212 | 0.53 | 0.77 | 34 | empty |
| 3 | 175 | 0.49 | 0.77 | 27 | empty |
| 4 | 105 | 0.42 | 0.77 | 18 | empty |
| 5 | 94 | 0.42 | 0.78 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1840 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1821 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 702 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 156 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 modified (engineered).
Compared structures
- 1SBZ · Crystal Structure of dodecameric FMN-dependent Ubix-like Decarboxylase from Escherichia… · the same entry in another collection · chain A against A, TM-score 1.00
- P69774 · AlphaFold monomer V2.0 prediction for probable ubix-like flavin prenyltransferase (P69774) · a predicted model of the same protein · chain D 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 P69774
- Elsewhere: RCSB PDB 1SBZ · PDBe 1SBZ · UniProt P69774
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