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Structure of the catalytic domain of an endo-1,3-beta-glucanase (laminarinase) from thermotoga petrophila rku-1

Analyse Structure of the catalytic domain of an endo-1,3-beta-glucanase (laminarinase)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4DFS
Type: protein
Length: 504 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycoside hydrolase, family 16
UniProt: A5IL44
Ligands: CA, SO4
Pockets: 2 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glycoside hydrolase, family 16	protein	252	7% helix, 49% strand	A5IL44

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	727	0.68	0.75	68	SO4
2	264	0.60	0.79	34	SO4

Interfaces

1 interface between chains.

A–B · 161 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4DFS · Structure of the catalytic domain of an endo-1,3-beta-glucanase (laminarinase) from… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt A5IL44
Elsewhere: RCSB PDB 4DFS · PDBe 4DFS · UniProt A5IL44

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