3ES6

Crystal structure of the novel complex formed between Zinc 2-glycoprotein (ZAG) and Prolactin inducible protein (PIP) from human seminal plasma


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the novel complex formed between zinc alpha2-glycoprotein (ZAG) and prolactin-inducible protein (PIP) from human seminal plasma

Hassan, M.I.Bilgrami, S.Kumar, V.Singh, N.Yadav, S.Kaur, P.Singh, T.P.

(2008) J.Mol.Biol. 384: 663-672

  • DOI: 10.1016/j.jmb.2008.09.072

  • PubMed Abstract: 
  • This is the first report on the formation of a complex between zinc alpha2-glycoprotein (ZAG) and prolactin-inducible protein (PIP). The complex was purified from human seminal plasma and crystallized using 20% polyethylene glycol 9000 and 5% hexaeth ...

    This is the first report on the formation of a complex between zinc alpha2-glycoprotein (ZAG) and prolactin-inducible protein (PIP). The complex was purified from human seminal plasma and crystallized using 20% polyethylene glycol 9000 and 5% hexaethylene glycol. The structure of the complex has been determined using X-ray crystallographic method and refined to an R(cryst) of 0.199 (R(free)=0.239). The structure of ZAG is broadly similar to the structure of serum ZAG. The scaffolding of PIP consists of seven beta-strands that are organized in the form of two antiparallel beta-pleated sheets, resulting in the formation of a sandwiched beta-sheet. The amino acid sequence of PIP contains one potential N-glycosylation site at Asn77, and the same is found glycosylated with four sugar residues. The structure of the complex shows that the beta-structure of PIP is ideally aligned with the beta-structure of domain alpha3 of ZAG to form a long interface between two proteins. The proximal beta-strands at the long interface are arranged in an antiparallel manner. There are 12 hydrogen bonds and three salt bridges between ZAG and PIP. At the two ends of vertical interface, two salt bridges are formed between pairs of Lys41-Asp233 and Lys68-Glu229. On the perpendicular interface involving alpha1-alpha2 domains of ZAG and a loop of PIP, another salt bridge is formed. The internal space at the corner of the L-shaped structure is filled with solvent molecules including a carbonate ion. The overall buried area in the complex is approximately 914 A(2), which is considerably higher than the 660 A(2) reported for the class I major histocompatibility complex structures.


    Organizational Affiliation

    Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Zinc-alpha-2-glycoprotein
A
278Homo sapiensMutation(s): 0 
Gene Names: AZGP1 (ZAG, ZNGP1)
Find proteins for P25311 (Homo sapiens)
Go to Gene View: AZGP1
Go to UniProtKB:  P25311
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Prolactin-inducible protein
B
118Homo sapiensMutation(s): 0 
Gene Names: PIP (GCDFP15, GPIP4)
Find proteins for P12273 (Homo sapiens)
Go to Gene View: PIP
Go to UniProtKB:  P12273
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
P6G
Query on P6G

Download SDF File 
Download CCD File 
A
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
NDG
Query on NDG

Download SDF File 
Download CCD File 
A, B
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CO3
Query on CO3

Download SDF File 
Download CCD File 
A
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 132.298α = 90.00
b = 132.298β = 90.00
c = 73.752γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance