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The apo structure of 3,4-dihydroxybenzoic acid decarboxylases from enterobacter cloacae
Analyse The apo structure of 3,4-dihydroxybenzoic acid decarboxylases from enterobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NY5
- Type
- protein
- Length
- 977 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3,4-dihydroxybenzoate decarboxylase
- UniProt
- B2DCZ6
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3,4-dihydroxybenzoate decarboxylase | protein | 489 | 28% helix, 25% strand | B2DCZ6 |
| B | 3,4-dihydroxybenzoate decarboxylase | protein | 488 | 28% helix, 27% strand | B2DCZ6 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.74 | 0.80 | 59 | empty |
| 2 | 690 | 0.73 | 0.79 | 46 | empty |
| 3 | 387 | 0.63 | 0.78 | 58 | empty |
| 4 | 208 | 0.48 | 0.75 | 32 | GOL |
| 5 | 82 | 0.40 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 537 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 5NY5 · The apo structure of 3,4-dihydroxybenzoic acid decarboxylases from Enterobacter cloacae · 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 B2DCZ6
- Elsewhere: RCSB PDB 5NY5 · PDBe 5NY5 · UniProt B2DCZ6
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