Research workbench
Crystal structure of the anaerobic desb-gallate complex
Analyse Crystal structure of the anaerobic desb-gallate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WR3
- Type
- protein
- Length
- 812 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gallate dioxygenase
- EC
- 1.13.11.-
- UniProt
- G2IKE5
- Ligands
- GDE, FE2
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gallate dioxygenase (EC 1.13.11.-) | protein | 407 | 43% helix, 14% strand | G2IKE5 |
| B | Gallate dioxygenase (EC 1.13.11.-) | protein | 405 | 47% helix, 16% strand | G2IKE5 |
Ligands and binding sites
- GDE · 3,4,5-trihydroxybenzoic acid · ligand · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.78 | 0.97 | 37 | GDE |
| 2 | 112 | 0.78 | 0.97 | 41 | empty |
| 3 | 361 | 0.69 | 0.81 | 54 | empty |
| 4 | 503 | 0.61 | 0.75 | 37 | empty |
| 5 | 142 | 0.59 | 0.84 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 4923 Ų buried · 89 hydrogen bonds · protein-protein
Compared structures
- 3WR3 · Crystal structure of the anaerobic DesB-gallate complex · 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 G2IKE5
- Elsewhere: RCSB PDB 3WR3 · PDBe 3WR3 · UniProt G2IKE5
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