Research workbench
Crystal structure of 2,6-dihydroxybenzoate decarboxylase from rhizobium
Analyse Crystal structure of 2,6-dihydroxybenzoate decarboxylase from rhizobium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DVT
- Type
- protein
- Length
- 1,293 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermophilic reversible gamma-resorcylate decarboxylase
- EC
- 4.1.1.-
- UniProt
- Q60GU1
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 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 | 51% helix, 13% strand | Q60GU1 |
| B | Thermophilic reversible gamma-resorcylate decarboxylase (EC 4.1.1.-) | protein | 324 | 51% helix, 13% strand | Q60GU1 |
| C | Thermophilic reversible gamma-resorcylate decarboxylase (EC 4.1.1.-) | protein | 323 | 50% helix, 13% strand | Q60GU1 |
| D | Thermophilic reversible gamma-resorcylate decarboxylase (EC 4.1.1.-) | protein | 321 | 51% helix, 13% strand | Q60GU1 |
Ligands and binding sites
- 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
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.74 | 0.97 | 26 | empty |
| 2 | 71 | 0.74 | 0.98 | 26 | empty |
| 3 | 453 | 0.70 | 0.81 | 50 | empty |
| 4 | 406 | 0.69 | 0.81 | 48 | empty |
| 5 | 558 | 0.68 | 0.78 | 42 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3500 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 3427 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 564 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 556 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 224 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2DVT · Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase from Rhizobium · 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 2DVT · PDBe 2DVT · UniProt Q60GU1
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