MolNFT v1 · #185002 · protein
Structure of lpmo domain of colonization factor gbpa from vibrio cholerae in the presence of potassium
7PB6 · Glcnac-binding protein a: “Structure of lpmo domain of colonization factor gbpa from vibrio cholerae in the presence of potassium”. X-ray diffraction, 3 ligands (K, CU, SCN), 3 pockets (best druggability 0.68). MolNFT v1 #185002 on…
- PDB
- 7PB6
- 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
- K, CU, SCN
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 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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