MolNFT v1 · #141510 · protein

A new PL6 alginate lyase complex with trisaccharide

5Z9T · Alginate lyase alyf-OU02: “A new PL6 alginate lyase complex with trisaccharide”. X-ray diffraction, 2 ligands (LGU, NA), 7 pockets (best druggability 0.74). MolNFT v1 #141510 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5Z9T
Type: protein
Length: 998 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alginate lyase alyf-OU02
Ligands: LGU, NA
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Alginate lyase alyf-OU02	protein	499	8% helix, 36% strand	—

Ligands and binding sites

LGU · alpha-L-gulopyranuronic acid · ligand · 6 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
MLI · Malonate ion · additive · 2 copies · chains A, B
GOL · Glycerol · additive · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	932	0.74	0.77	96	GOL
2	262	0.64	0.82	38	LGU, MLI
3	252	0.62	0.81	38	LGU, MLI
4	94	0.47	0.80	17	empty
5	108	0.46	0.79	20	empty

Interfaces

1 interface between chains.

A–B · 610 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5Z9T · a new PL6 alginate lyase complex with trisaccharide · 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 5Z9T · PDBe 5Z9T

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