Research workbench
Crystal structure of SACOL2612 - COCE/NOND family hydrolase from staphylococcus aureus
Analyse Crystal structure of SACOL2612 - COCE/NOND family hydrolase from staphylococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IB3
- Type
- protein
- Length
- 1,103 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- COCE/NOND family hydrolase
- UniProt
- Q5HCV6
- Ligands
- PLM, NI, CL
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | COCE/NOND family hydrolase | protein | 551 | 19% helix, 36% strand | Q5HCV6 |
| B | COCE/NOND family hydrolase | protein | 552 | 20% helix, 36% strand | Q5HCV6 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A
- NI · Nickel (II) ion · metal · chains B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.87 | 0.88 | 107 | empty |
| 2 | 982 | 0.75 | 0.77 | 102 | PLM |
| 3 | 90 | 0.44 | 0.80 | 18 | empty |
| 4 | 75 | 0.40 | 0.79 | 20 | empty |
| 5 | 78 | 0.35 | 0.76 | 21 | CL |
Interfaces
1 interface between chains.
- A–B · 1438 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3IB3 · Crystal Structure of SACOL2612 - CocE/NonD family hydrolase from Staphylococcus aureus · 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 Q5HCV6
- Elsewhere: RCSB PDB 3IB3 · PDBe 3IB3 · UniProt Q5HCV6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.