MolNFT v1 · #120638 · protein

Structure of alginate-binding protein ALGQ2 in complex with an alginate pentasaccharide

5H6U: “Structure of alginate-binding protein ALGQ2 in complex with an alginate pentasaccharide”. X-ray diffraction, 2 ligands (BEM, CA), 4 pockets (best druggability 0.85). MolNFT v1 #120638 on GenesisL1: 3D structure, binding sites and…

PDB: 5H6U
Type: protein
Length: 972 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ALGQ2
UniProt: Q9KWT5
Ligands: BEM, CA
Pockets: 4 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ALGQ2	protein	487	45% helix, 14% strand	Q9KWT5
B	ALGQ2	protein	485	46% helix, 15% strand	Q9KWT5

Ligands and binding sites

BEM · beta-D-mannopyranuronic acid · sugar · 10 copies · chains A, B
CA · Calcium ion · metal · 6 copies · chains A, B

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	929	0.85	0.86	85	BEM
2	1118	0.83	0.84	102	BEM, CA
3	113	0.44	0.77	17	empty
4	78	0.30	0.73	20	empty

Interfaces

1 interface between chains.

A–B · 892 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5H6U · Structure of alginate-binding protein AlgQ2 in complex with an alginate pentasaccharide · 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 Q9KWT5
Elsewhere: RCSB PDB 5H6U · PDBe 5H6U · UniProt Q9KWT5

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