MolNFT v1 · #123013 · protein

Crystal structure of PA14 domain of mpafp antifreeze protein

5J6Y: “Crystal structure of PA14 domain of mpafp antifreeze protein”. X-ray diffraction, 3 ligands (GLC, BGC, CA), 1 pocket (best druggability 0.23). MolNFT v1 #123013 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5J6Y
Type: protein
Length: 188 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antifreeze protein
UniProt: A1YIY3
Ligands: GLC, BGC, CA
Pockets: 1 · best druggability 0.23

Structure

x-ray diffraction · 1 distinct chain · 12% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antifreeze protein	protein	188	12% helix, 43% strand	A1YIY3

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · chains A
BGC · beta-D-glucopyranose · sugar · chains A
CA · Calcium ion · metal · 8 copies · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	50	0.23	0.72	16	empty

Compared structures

5J6Y · Crystal structure of PA14 domain of MpAFP Antifreeze protein · 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 A1YIY3
Elsewhere: RCSB PDB 5J6Y · PDBe 5J6Y · UniProt A1YIY3

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