Research workbench
Crystal structure of ALPHA/BETA superfamily hydrolase from oenococcus oeni psu-1
Analyse Crystal structure of ALPHA/BETA superfamily hydrolase from oenococcus oeni psu-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FSG
- Type
- protein
- Length
- 1,063 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALPHA/BETA superfamily hydrolase
- UniProt
- Q04D10
- Ligands
- SO4, CL
- Pockets
- 13 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ALPHA/BETA superfamily hydrolase | protein | 267 | 40% helix, 18% strand | Q04D10 |
| B, C | ALPHA/BETA superfamily hydrolase | protein | 266 | 39% helix, 18% strand | Q04D10 |
| D | ALPHA/BETA superfamily hydrolase | protein | 264 | 41% helix, 18% strand | Q04D10 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.67 | 0.88 | 24 | EDO |
| 2 | 237 | 0.57 | 0.78 | 27 | SO4 |
| 3 | 193 | 0.55 | 0.79 | 24 | SO4 |
| 4 | 200 | 0.53 | 0.78 | 24 | SO4 |
| 5 | 159 | 0.52 | 0.79 | 23 | SO4 |
Interfaces
3 interfaces between chains.
- A–C · 1079 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1078 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 468 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered, oxidation).
Compared structures
- 3FSG · Crystal structure of alpha/beta superfamily hydrolase from Oenococcus oeni PSU-1 · 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 Q04D10
- Elsewhere: RCSB PDB 3FSG · PDBe 3FSG · UniProt Q04D10
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