Research workbench
Crystal structure of the anaerobic H124F desb-gallate complex
Analyse Crystal structure of the anaerobic H124F 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
- 3WRB
- Type
- protein
- Length
- 820 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gallate dioxygenase
- EC
- 1.13.11.58
- UniProt
- Q5NTE5
- Ligands
- GDE, FE2
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gallate dioxygenase (EC 1.13.11.58) | protein | 409 | 45% helix, 15% strand | Q5NTE5 |
| B | Gallate dioxygenase (EC 1.13.11.58) | protein | 411 | 45% helix, 15% strand | Q5NTE5 |
Ligands and binding sites
- GDE · 3,4,5-trihydroxybenzoic acid · ligand · 2 copies · 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.76 | 0.87 | 65 | GDE |
| 2 | 400 | 0.74 | 0.84 | 71 | GDE |
| 3 | 474 | 0.62 | 0.75 | 42 | empty |
| 4 | 90 | 0.49 | 0.82 | 26 | empty |
| 5 | 92 | 0.48 | 0.82 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 5026 Ų buried · 104 hydrogen bonds · protein-protein
Compared structures
- 3WRB · Crystal structure of the anaerobic H124F 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 Q5NTE5
- Elsewhere: RCSB PDB 3WRB · PDBe 3WRB · UniProt Q5NTE5
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