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Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase Complexed with 2,6-Dihydroxybenzoate
Analyse Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase Complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DVU
- Type
- protein
- Length
- 1,294 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Rhizobium sp.
- Molecule
- Thermophilic reversible gamma-resorcylate decarboxylase
- EC
- 4.1.1.-
- UniProt
- Q60GU1
- Ligands
- GRE, ZN
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.9 · 4 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermophilic reversible gamma-resorcylate decarboxylase (EC 4.1.1.-) | protein | 325 | 52% helix, 13% strand | Q60GU1 |
| B | Thermophilic reversible gamma-resorcylate decarboxylase (EC 4.1.1.-) | protein | 324 | 52% helix, 13% strand | Q60GU1 |
| C | Thermophilic reversible gamma-resorcylate decarboxylase (EC 4.1.1.-) | protein | 324 | 50% helix, 12% strand | Q60GU1 |
| D | Thermophilic reversible gamma-resorcylate decarboxylase (EC 4.1.1.-) | protein | 321 | 51% helix, 13% strand | Q60GU1 |
Ligands and binding sites
- GRE · 2,6-dihydroxybenzoic acid · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.74 | 0.97 | 28 | empty |
| 2 | 71 | 0.72 | 0.97 | 26 | empty |
| 3 | 502 | 0.68 | 0.78 | 43 | GRE |
| 4 | 542 | 0.67 | 0.77 | 45 | GRE |
| 5 | 102 | 0.62 | 0.88 | 27 | GRE |
Interfaces
6 interfaces between chains.
- A–B · 3512 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 3446 Ų buried · 51 hydrogen bonds · protein-protein
- A–C · 558 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 550 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 227 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2DVU · Crystal structure of 2,6-dihydroxybenzoate decarboxylase complexed with… · 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 Q60GU1
- Elsewhere: RCSB PDB 2DVU · PDBe 2DVU · UniProt Q60GU1
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