MolNFT v1 · #59310 · protein
Crystal structure and biochemical characterization of gdosp, a gentisate 1,2-dioxygenase from silicibacter pomeroyi
3BU7: “Crystal structure and biochemical characterization of gdosp, a gentisate 1,2-dioxygenase from silicibacter…”. X-ray diffraction, 1 ligand (FE2), 8 pockets (best druggability 0.63). MolNFT v1 #59310 on GenesisL1: 3D structure…
- PDB
- 3BU7
- Type
- protein
- Length
- 713 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gentisate 1,2-dioxygenase
- EC
- 1.13.11.4
- UniProt
- Q5LLB1
- Ligands
- FE2
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gentisate 1,2-dioxygenase (EC 1.13.11.4) | protein | 355 | 19% helix, 32% strand | Q5LLB1 |
| B | Gentisate 1,2-dioxygenase (EC 1.13.11.4) | protein | 358 | 18% helix, 32% strand | Q5LLB1 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 4 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.63 | 0.79 | 40 | empty |
| 2 | 291 | 0.59 | 0.78 | 44 | FE2 |
| 3 | 316 | 0.59 | 0.77 | 42 | empty |
| 4 | 288 | 0.57 | 0.77 | 36 | FE2 |
| 5 | 259 | 0.55 | 0.77 | 32 | FE2 |
Interfaces
1 interface between chains.
- A–B · 1508 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3BU7 · Crystal Structure and Biochemical Characterization of GDOsp, a Gentisate 1,2-Dioxygenase… · 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 Q5LLB1
- Elsewhere: RCSB PDB 3BU7 · PDBe 3BU7 · UniProt Q5LLB1
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