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Formylglycine generating enzyme from streptomyces coelicolor
Analyse Formylglycine generating enzyme from streptomyces coelicolor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q17
- Type
- protein
- Length
- 1,438 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formylglycine generating enzyme
- UniProt
- Q9F3C7
- Ligands
- CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 18% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formylglycine generating enzyme | protein | 288 | 18% helix, 22% strand | Q9F3C7 |
| B | Formylglycine generating enzyme | protein | 288 | 18% helix, 23% strand | Q9F3C7 |
| C | Formylglycine generating enzyme | protein | 287 | 18% helix, 23% strand | Q9F3C7 |
| D | Formylglycine generating enzyme | protein | 286 | 18% helix, 22% strand | Q9F3C7 |
| E | Formylglycine generating enzyme | protein | 289 | 18% helix, 22% strand | Q9F3C7 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.81 | 0.82 | 100 | empty |
| 2 | 985 | 0.79 | 0.80 | 88 | empty |
| 3 | 618 | 0.78 | 0.84 | 56 | empty |
| 4 | 362 | 0.66 | 0.80 | 32 | empty |
| 5 | 136 | 0.54 | 0.82 | 26 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1038 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 952 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 636 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 359 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 268 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2Q17 · Formylglycine Generating Enzyme from Streptomyces coelicolor · the same entry in another collection · chain E against E, TM-score 1.00
- Q9F3C7 · AlphaFold monomer V2.0 prediction for formylglycine-generating enzyme (Q9F3C7) · a predicted model of the same protein · chain D 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 Q9F3C7
- Elsewhere: RCSB PDB 2Q17 · PDBe 2Q17 · UniProt Q9F3C7
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