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Crystal structure of DLN1 complexed with MAN(ALPHA1-3)MAN

Analyse Crystal structure of DLN1 complexed with MAN(ALPHA1-3)MAN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZNR
Type: protein
Length: 636 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Natterin-like protein
UniProt: Q5CZR5
Ligands: MAN, CL
Pockets: 9 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 63% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Natterin-like protein	protein	318	3% helix, 63% strand	Q5CZR5

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
PGE · Triethylene glycol · additive · 4 copies · chains A, B
PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
1PE · Pentaethylene glycol · additive · chains A, B

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

Pockets

9 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	75	0.50	0.84	20	empty
2	111	0.49	0.80	23	PGE
3	85	0.39	0.78	21	empty
4	99	0.39	0.77	25	empty
5	109	0.39	0.75	25	empty

Interfaces

1 interface between chains.

A–B · 1594 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

4ZNR · Crystal structure of Dln1 complexed with Man(alpha1-3)Man · the same entry in another collection · chain A against A, TM-score 1.00
Q5CZR5 · AlphaFold monomer V2.0 prediction for aerolysin-like protein (Q5CZR5) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q5CZR5
Elsewhere: RCSB PDB 4ZNR · PDBe 4ZNR · UniProt Q5CZR5

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