MolNFT v1 · #157295 · protein
Formylglycine generating enzyme bound to copper
6MUJ · Formylglycine-generating enzyme: “Formylglycine generating enzyme bound to copper”. X-ray diffraction, 3 ligands (GLY, CU, CA), 18 pockets (best druggability 0.81). MolNFT v1 #157295 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6MUJ
- Type
- protein
- Length
- 1,456 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formylglycine-generating enzyme
- EC
- 1.8.3.7
- UniProt
- Q9F3C7
- Ligands
- GLY, CU, CA
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Formylglycine-generating enzyme (EC 1.8.3.7) | protein | 289 | 18% helix, 22% strand | Q9F3C7 |
| B | Formylglycine-generating enzyme (EC 1.8.3.7) | protein | 294 | 16% helix, 23% strand | Q9F3C7 |
| D | Formylglycine-generating enzyme (EC 1.8.3.7) | protein | 293 | 18% helix, 23% strand | Q9F3C7 |
| E | Formylglycine-generating enzyme (EC 1.8.3.7) | protein | 291 | 18% helix, 22% strand | Q9F3C7 |
Ligands and binding sites
- GLY · Glycine · ligand · chains D
- CU · Copper (II) ion · metal · 20 copies · chains A, B, C, D, E
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D, E
- IMD · Imidazole · additive · 4 copies · chains A, B, D, E
- GOL · Glycerol · additive · 4 copies · chains C, A, D
- FMT · Formic acid · additive · chains C
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.81 | 0.83 | 79 | empty |
| 2 | 682 | 0.80 | 0.84 | 66 | empty |
| 3 | 845 | 0.80 | 0.82 | 85 | DTT |
| 4 | 241 | 0.67 | 0.85 | 29 | IMD |
| 5 | 254 | 0.52 | 0.75 | 30 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1026 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 1021 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 689 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 589 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 251 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 Q9F3C7
- Elsewhere: RCSB PDB 6MUJ · PDBe 6MUJ · UniProt Q9F3C7
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