Research workbench
Ycac from pseudomonas aeruginosa with S-mercaptocysteine active site cysteine
Analyse Ycac from pseudomonas aeruginosa with S-mercaptocysteine active site cysteine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WH0
- Type
- protein
- Length
- 1,616 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative hydrolase
- UniProt
- Q02J38
- Ligands
- CL
- Pockets
- 20 · best druggability 0.81
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 | Putative hydrolase | protein | 202 | 51% helix, 18% strand | Q02J38 |
Ligands and binding sites
- 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 | 971 | 0.81 | 0.83 | 138 | empty |
| 2 | 1012 | 0.76 | 0.78 | 97 | empty |
| 3 | 622 | 0.76 | 0.82 | 86 | empty |
| 4 | 864 | 0.75 | 0.79 | 84 | empty |
| 5 | 197 | 0.75 | 0.91 | 49 | empty |
Interfaces
20 interfaces between chains.
- B–C · 1438 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1432 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1424 Ų buried · 14 hydrogen bonds · protein-protein
- E–H · 1424 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 1423 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered, oxidation).
Compared structures
- 4WH0 · YcaC from Pseudomonas aeruginosa with S-mercaptocysteine active site cysteine · the same entry in another collection · chain C against C, 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 Q02J38
- Elsewhere: RCSB PDB 4WH0 · PDBe 4WH0 · UniProt Q02J38
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