Research workbench
Ycac from pseudomonas aeruginosa with hexane-2,5-diol and covalent acrylamide
Analyse Ycac from pseudomonas aeruginosa with hexane-2,5-diol and covalent acrylamide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WGF
- Type
- protein
- Length
- 1,616 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable hydrolase
- UniProt
- Q9I4D6
- Ligands
- ROP, HX2, SO4, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Probable hydrolase | protein | 202 | 51% helix, 18% strand | Q9I4D6 |
Ligands and binding sites
- ROP · Propionamide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- HX2 · (2R,5R)-hexane-2,5-diol · ligand · 8 copies · chains A, E, B, H, C, G, D, F
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.80 | 0.85 | 107 | empty |
| 2 | 617 | 0.80 | 0.85 | 102 | empty |
| 3 | 495 | 0.74 | 0.82 | 31 | empty |
| 4 | 553 | 0.74 | 0.82 | 36 | empty |
| 5 | 227 | 0.73 | 0.88 | 51 | HX2 |
Interfaces
20 interfaces between chains.
- E–F · 1451 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1430 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1430 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 1426 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1425 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified, 9 covalent (engineered, covalent ligand).
Compared structures
- 4WGF · YcaC from Pseudomonas aeruginosa with hexane-2,5-diol and covalent acrylamide · 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 Q9I4D6
- Elsewhere: RCSB PDB 4WGF · PDBe 4WGF · UniProt Q9I4D6
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