Research workbench
Structure of LPMO domain of colonization factor GbpA from Vibrio cholerae in the presence of potassium
Analyse Structure of LPMO domain of colonization factor GbpA from Vibrio cholerae in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PB6
- Type
- protein
- Length
- 360 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- Vibrio cholerae O1
- Molecule
- GlcNAc-binding protein A
- UniProt
- Q9KLD5
- Ligands
- K, CU, SCN
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · resolution 1.5 · 1 distinct chain · 10% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GlcNAc-binding protein A | protein | 180 | 10% helix, 37% strand | Q9KLD5 |
Ligands and binding sites
- K · Potassium ion · metal · 7 copies · chains A, B
- CU · Copper (II) ion · metal · 2 copies · chains A, B
- SCN · Thiocyanate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.68 | 0.95 | 15 | empty |
| 2 | 101 | 0.38 | 0.75 | 26 | empty |
| 3 | 58 | 0.25 | 0.72 | 17 | K |
Interfaces
1 interface between chains.
- A–B · 545 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7PB6 · Structure of lpmo domain of colonization factor gbpa from vibrio cholerae in the presence… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KLD5 · AlphaFold monomer V2.0 prediction for glcnac-binding protein a (Q9KLD5) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9KLD5
- Elsewhere: RCSB PDB 7PB6 · PDBe 7PB6 · UniProt Q9KLD5
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