Research workbench
Crystal structure of the desb-gallate complex exposed to aerobic atomosphere
Analyse Crystal structure of the desb-gallate complex exposed to aerobic atomosphere in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WRA
- Type
- protein
- Length
- 812 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gallate dioxygenase
- EC
- 1.13.11.58
- UniProt
- Q5NTE5
- Ligands
- FE2
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gallate dioxygenase (EC 1.13.11.58) | protein | 408 | 45% helix, 15% strand | Q5NTE5 |
| B | Gallate dioxygenase (EC 1.13.11.58) | protein | 404 | 46% helix, 16% strand | Q5NTE5 |
Ligands and binding sites
- 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
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.71 | 0.80 | 60 | empty |
| 2 | 444 | 0.68 | 0.80 | 53 | empty |
| 3 | 441 | 0.60 | 0.75 | 36 | empty |
| 4 | 162 | 0.50 | 0.78 | 36 | empty |
| 5 | 88 | 0.45 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 4537 Ų buried · 98 hydrogen bonds · protein-protein
Compared structures
- 3WRA · Crystal structure of the desB-Gallate complex exposed to Aerobic Atomosphere · 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 3WRA · PDBe 3WRA · UniProt Q5NTE5
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