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Crystal structure of Rhagium Mordax antifreeze protein

Analyse Crystal structure of Rhagium Mordax antifreeze protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XNR
Type: protein
Length: 689 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.05
Source: Rhagium mordax
Molecule: Antifreeze protein
Pockets: 4 · best druggability 0.37

Structure

x-ray diffraction · resolution 2.05 · 3 distinct chains · 0% helix, 69% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
AAA	Antifreeze protein	protein	139	0% helix, 68% strand	—
BBB, CCC, EEE	Antifreeze protein	protein	138	0% helix, 70% strand	—
DDD	Antifreeze protein	protein	136	0% helix, 69% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 3 copies · chains BBB, CCC, DDD, EEE

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	76	0.37	0.77	26	empty
2	75	0.36	0.77	26	empty
3	54	0.32	0.77	17	empty
4	77	0.31	0.74	25	empty

Interfaces

2 interfaces between chains.

BBB–CCC · 1187 Å² buried · 14 hydrogen bonds · protein-protein
DDD–EEE · 1160 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6XNR · PDBe 6XNR

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