MolNFT v1 · #170006 · protein
Crystal structure reveals non-coordinative binding of O2 to the copper center of the formylglycine-generating enzyme - FGE:AG:S:NO complex
6XTN: “Crystal structure reveals non-coordinative binding of O2 to the copper center of the formylglycine-generating…”. X-ray diffraction, 5 ligands (SOA, CA, AG), 3 pockets (best druggability 0.44). MolNFT v1 #170006 on GenesisL1: 3D…
- PDB
- 6XTN
- Type
- protein
- Length
- 319 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formylglycine-generating enzyme; Abz-ala-thr-thr-pro-leu-cys-gly-pro-ser-arg-ala-ser-ile…
- EC
- 1.8.3.7
- UniProt
- D1A7C3
- Ligands
- SOA, CA, AG, CL, NO
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formylglycine-generating enzyme (EC 1.8.3.7) | protein | 303 | 18% helix, 20% strand | D1A7C3 |
| C | Abz-ala-thr-thr-pro-leu-cys-gly-pro-ser-arg-ala-ser-ile- leu-ser-gly | protein | 16 | 19% helix, 0% strand | — |
Ligands and binding sites
- SOA · Isatoic anhydride · ligand · chains A, C
- CA · Calcium ion · metal · 2 copies · chains A
- AG · Silver ion · metal · chains A, C
- CL · Chloride ion · ion · chains A
- NO · Nitric oxide · ion · chains A, C
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.44 | 0.78 | 21 | empty |
| 2 | 109 | 0.37 | 0.74 | 24 | empty |
| 3 | 111 | 0.36 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–C · 842 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6XTN · Crystal structure reveals non-coordinative binding of O2 to the copper center of the… · the same entry in another collection · chain A against A, TM-score 1.00
- D1A7C3 · AlphaFold monomer V2.0 prediction for formylglycine-generating enzyme (D1A7C3) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 D1A7C3
- Elsewhere: RCSB PDB 6XTN · PDBe 6XTN · UniProt D1A7C3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.