Research workbench
Crystal structure of the anaerobic desb-gallate complex by co- crystallization
Analyse Crystal structure of the anaerobic desb-gallate complex by co- crystallization in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WPM
- Type
- protein
- Length
- 813 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, FE
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gallate dioxygenase (EC 1.13.11.-) | protein | 408 | 43% helix, 14% strand | G2IKE5 |
| B | Gallate dioxygenase (EC 1.13.11.-) | protein | 405 | 45% helix, 16% strand | G2IKE5 |
Ligands and binding sites
- GDE · 3,4,5-trihydroxybenzoic acid · ligand · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.74 | 0.97 | 29 | GDE |
| 2 | 77 | 0.74 | 0.97 | 30 | empty |
| 3 | 307 | 0.66 | 0.82 | 57 | empty |
| 4 | 54 | 0.64 | 0.94 | 18 | empty |
| 5 | 462 | 0.61 | 0.76 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 4948 Ų buried · 88 hydrogen bonds · protein-protein
Compared structures
- 3WPM · Crystal structure of the anaerobic DesB-gallate complex by co-crystallization · 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 3WPM · PDBe 3WPM · UniProt G2IKE5
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