Research workbench
Hydrolytic catalysis and structural stabilization in a designed metalloprotein
Analyse Hydrolytic catalysis and structural stabilization in a designed metalloprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PBJ
- Type
- protein
- Length
- 172 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coil ser L9L-pen L23H
- Ligands
- ACE, ZN, HG, NA, CL, NH2
Structure
x-ray diffraction · 2 distinct chains · 89% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Coil ser L9L-pen L23H | protein | 29 | 90% helix, 0% strand | — |
| B, F | Coil ser L9L-pen L23H | protein | 28 | 89% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 5 copies · chains B, C, D, E, F
- ZN · Zinc ion · metal · 7 copies · chains A, B, C, D, E, F
- HG · Mercury (II) ion · metal · 2 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · chains B, E
- CL · Chloride ion · ion · 3 copies · chains A, B, C, E, F
- NH2 · Amino group · ion · 2 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
7 interfaces between chains.
- A–C · 625 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 618 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 593 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 591 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 586 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 5 covalent (nonstandard, covalent ligand).
Compared structures
- 3PBJ · Hydrolytic catalysis and structural stabilization in a designed metalloprotein · 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
- Elsewhere: RCSB PDB 3PBJ · PDBe 3PBJ
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.