Research workbench
Structure of lpmo domain of colonization factor gbpa from vibrio cholerae in the presence of calcium
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
- 7PB7
- Type
- protein
- Length
- 360 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glcnac-binding protein a
- UniProt
- Q9KLD5
- Ligands
- CU, CA
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glcnac-binding protein a | protein | 180 | 12% helix, 37% strand | Q9KLD5 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.71 | 0.83 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 334 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7PB7 · 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 7PB7 · PDBe 7PB7 · UniProt Q9KLD5
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