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Crystal structure of the catalytic domain of a multi-domain alginate lyase DP0100 from thermophilic bacterium defluviitalea phaphyphila

Analyse Crystal structure of the catalytic domain of a multi-domain alginate lyase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JPH
Type: protein
Length: 770 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alginate lyase
Ligands: BEM, CA, MN, MG
Pockets: 4 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alginate lyase	protein	770	27% helix, 29% strand	—

Ligands and binding sites

BEM · beta-D-mannopyranuronic acid · sugar · 3 copies · chains A
CA · Calcium ion · metal · 2 copies · chains A
MN · Manganese (II) ion · metal · chains A
MG · Magnesium ion · metal · chains A
ACT · Acetate ion · additive · chains A

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

Pockets

4 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	324	0.53	0.74	43	BEM, ACT, MG
2	241	0.53	0.76	27	empty
3	182	0.46	0.75	21	empty
4	121	0.43	0.76	20	empty

Compared structures

6JPH · Crystal structure of the catalytic domain of a multi-domain alginate lyase Dp0100 from… · 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
Elsewhere: RCSB PDB 6JPH · PDBe 6JPH

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