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Crystal structure of bovine C-lobe with fructose at 3.0 A resolution

Analyse Crystal structure of bovine C-lobe with fructose at 3.0 A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2O51
Type: protein
Length: 341 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3
Source: Bos taurus
Molecule: Lactotransferrin
EC: 3.4.21.-
UniProt: P24627
Ligands: NAG, BMA, MAN, FRU, ZN, FE, CO3, SO4
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · resolution 3 · 1 distinct chain · 32% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lactotransferrin (EC 3.4.21.-)	protein	341	32% helix, 17% strand	P24627

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
BMA · beta-D-mannopyranose · sugar · 2 copies
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
FRU · beta-D-fructofuranose · sugar · chains A
ZN · Zinc ion · metal · 2 copies · chains A
FE · Fe (III) ion · metal · chains A
CO3 · Carbonate ion · ion · chains A
SO4 · Sulfate ion · ion · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	250	0.75	0.89	41	empty
2	119	0.41	0.76	24	empty
3	92	0.33	0.73	22	NAG
4	67	0.32	0.75	20	empty

Modifications

Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

2O51 · Crystal structure of bovine C-lobe with fructose at 3.0 a resolution · the same entry in another collection · chain A against A, TM-score 1.00
P24627 · AlphaFold monomer V2.0 prediction for lactotransferrin (P24627) · a predicted model of the same protein · chain A 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 P24627
Elsewhere: RCSB PDB 2O51 · PDBe 2O51 · UniProt P24627

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