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Crystal structure of GNK2 complexed with mannose

Analyse Crystal structure of GNK2 complexed with mannose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XRE
Type: protein
Length: 432 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antifungal protein ginkbilobin-2
UniProt: A4ZDL6
Ligands: MAN
Pockets: 4 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Antifungal protein ginkbilobin-2	protein	108	29% helix, 30% strand	A4ZDL6

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 2 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	173	0.52	0.79	22	empty
2	133	0.49	0.79	20	empty
3	138	0.44	0.76	19	empty
4	79	0.36	0.77	15	empty

Interfaces

4 interfaces between chains.

B–C · 636 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 610 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 122 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 95 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

4XRE · Crystal structure of Gnk2 complexed with mannose · the same entry in another collection · chain A against A, TM-score 1.00
A4ZDL6 · AlphaFold monomer V2.0 prediction for antifungal protein ginkbilobin-2 (A4ZDL6) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 A4ZDL6
Elsewhere: RCSB PDB 4XRE · PDBe 4XRE · UniProt A4ZDL6

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