MolNFT v1 · #170004 · protein
Crystal structure reveals non-coordinative binding of O2 to the copper center of the formylglycine-generating enzyme - FGE:AG:S complex
6XTL: “Crystal structure reveals non-coordinative binding of O2 to the copper center of the formylglycine-generating…”. X-ray diffraction, 4 ligands (SOA, CA, AG), 4 pockets (best druggability 0.41). MolNFT v1 #170004 on GenesisL1: 3D…
- PDB
- 6XTL
- Type
- protein
- Length
- 317 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
- Pockets
- 4 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 19% 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 | 14 | 21% 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
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.41 | 0.79 | 23 | empty |
| 2 | 98 | 0.35 | 0.74 | 23 | empty |
| 3 | 100 | 0.34 | 0.73 | 21 | empty |
| 4 | 50 | 0.34 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–C · 847 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6XTL · 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 6XTL · PDBe 6XTL · UniProt D1A7C3
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