Research workbench
Crystal structure of notched-fin eelpout type III antifreeze protein (NFE6, afp), P212121 form
Analyse Crystal structure of notched-fin eelpout type III antifreeze protein (NFE6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XQP
- Type
- protein
- Length
- 259 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ice-structuring protein
- UniProt
- Q53UJ4
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Ice-structuring protein | protein | 65 | 20% helix, 25% strand | Q53UJ4 |
| C | Ice-structuring protein | protein | 64 | 19% helix, 25% strand | Q53UJ4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.43 | 0.74 | 36 | empty |
Interfaces
4 interfaces between chains.
- A–B · 439 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 245 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 100 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 12 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5XQP · Crystal structure of Notched-fin eelpout type III antifreeze protein (NFE6, AFP), P212121… · 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
- Every structure of UniProt Q53UJ4
- Elsewhere: RCSB PDB 5XQP · PDBe 5XQP · UniProt Q53UJ4
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