MolNFT v1 · #83521 · protein
Crystal structure of the anaerobic desb-gallate complex
3WKU · Gallate dioxygenase: “Crystal structure of the anaerobic desb-gallate complex”. X-ray diffraction, 2 ligands (GDE, FE), 9 pockets (best druggability 0.74). MolNFT v1 #83521 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3WKU
- 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
- G2IKE5
- Ligands
- GDE, FE
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gallate dioxygenase (EC 1.13.11.58) | protein | 407 | 41% helix, 14% strand | G2IKE5 |
| B | Gallate dioxygenase (EC 1.13.11.58) | protein | 405 | 46% 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.74 | 0.89 | 57 | FE |
| 2 | 54 | 0.68 | 0.96 | 21 | GDE |
| 3 | 724 | 0.67 | 0.75 | 68 | empty |
| 4 | 145 | 0.59 | 0.83 | 24 | empty |
| 5 | 66 | 0.47 | 0.84 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 4987 Ų buried · 97 hydrogen bonds · protein-protein
Compared structures
- 3WKU · 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 3WKU · PDBe 3WKU · UniProt G2IKE5
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