Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.83 kDa 
• Atom Count: 2274 
• Residue Count: 273 
• Unique protein chains: 1

1T7Z

Zn-alpha-2-glycoprotein; baculo-ZAG no PEG, no glycerol

• DOI: 10.2210/pdb1T7Z/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2004-05-11 Released: 2004-12-21 
• Deposition Author(s): Delker, S.L., West Jr., A.P., McDermott, L., Kennedy, M.W., Bjorkman, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.268 
• R-Value Work: 0.217 

Literature

Crystallographic studies of ligand binding by Zn-alpha2-glycoprotein.

Delker, S.L., West Jr., A.P., McDermott, L., Kennedy, M.W., Bjorkman, P.J.

(2004) J Struct Biol 148: 205-213

• PubMed: 15477100 
• DOI: 10.1016/j.jsb.2004.04.009
• Primary Citation of Related Structures:  
  1T80, 1T7Z, 1T7Y, 1T7X, 1T7W, 1T7V


• PubMed Abstract: 
  

Zn-alpha2-glycoprotein (ZAG) is a 41 kDa soluble protein that is present in most bodily fluids. The previously reported 2.8 A crystal structure of ZAG isolated from human serum demonstrated the structural similarity between ZAG and class I major histocompatibility complex (MHC) molecules and revealed a non-peptidic ligand in the ZAG counterpart of the MHC peptide-binding groove. Here we present crystallographic studies to explore further the nature of the non-peptidic ligand in the ZAG groove. Comparison of the structures of several forms of recombinant ZAG, including a 1.95 A structure derived from ZAG expressed in insect cells, suggests that the non-peptidic ligand in the current structures and in the structure of serum ZAG is a polyethylene glycol (PEG), which is present in the crystallization conditions used. Further support for PEG binding in the ZAG groove is provided by the finding that PEG displaces a fluorophore-tagged fatty acid from the ZAG binding site. From these results we hypothesize that our purified forms of ZAG do not contain a bound endogenous ligand, but that the ZAG groove is capable of binding hydrophobic molecules, which may relate to its function.

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Related Citations: 

• Crystal structure of human ZAG, a fat-depleting factor related to MHC molecules
  Sanchez, L.M., Chirino, A.J., Bjorkman, P.J.
  (1999) Science 283: 1914

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Organizational Affiliation: 

Division of Biology, 114-96 Pasadena, CA 91125, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc-alpha-2-glycoprotein	A	278	Homo sapiens	Mutation(s): 2  Gene Names: AZGP1, ZAG, ZNGP1
Find proteins for P25311 (Homo sapiens) Explore P25311  Go to UniProtKB:  P25311
NIH Common Fund Data Resources
PHAROS  P25311 GTEx  ENSG00000160862

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.268 
• R-Value Work: 0.217 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.084	α = 90
b = 122.084	β = 90
c = 65.415	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-11 
• Released Date: 2004-12-21 
Deposition Author(s): Delker, S.L., West Jr., A.P., McDermott, L., Kennedy, M.W., Bjorkman, P.J.

Revision History 

• Version 1.0: 2004-12-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary