Research workbench
Revealing surface waters on an antifreeze protein by fusion protein crystallography
Analyse Revealing surface waters on an antifreeze protein by fusion protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C7R
- Type
- protein
- Length
- 870 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion protein of maltose-binding periplasmic protein and type-3 ice-structuring protein…
- UniProt
- P0AEY0, P19614
- Ligands
- GLC, SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fusion protein of maltose-binding periplasmic protein and type-3 ice-structuring protein hplc 12 | protein | 435 | 42% helix, 22% strand | P0AEY0, P19614 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.75 | 0.83 | 52 | GLC |
| 2 | 456 | 0.75 | 0.84 | 50 | SO4 |
| 3 | 624 | 0.74 | 0.81 | 64 | GLC |
| 4 | 320 | 0.58 | 0.77 | 40 | empty |
| 5 | 213 | 0.53 | 0.78 | 26 | SO4 |
Interfaces
1 interface between chains.
- A–B · 579 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5C7R · Revealing surface waters on an antifreeze protein by fusion protein crystallography · the same entry in another collection · chain A against A, TM-score 1.00
- P19614 · AlphaFold monomer V2.0 prediction for type-3 ice-structuring protein hplc 12 (P19614) · a predicted model of the same protein · chain B against A, TM-score 0.15
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 P0AEY0
- Every structure of UniProt P19614
- Elsewhere: RCSB PDB 5C7R · PDBe 5C7R · UniProt P0AEY0 · UniProt P19614
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