1KX1

Rat mannose protein A complexed with Man6-GlcNAc2-Asn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 

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This is version 2.0 of the entry. See complete history


Literature

Orientation of bound ligands in mannose-binding proteins. Implications for multivalent ligand recognition.

Ng, K.K.Kolatkar, A.R.Park-Snyder, S.Feinberg, H.Clark, D.A.Drickamer, K.Weis, W.I.

(2002) J Biol Chem 277: 16088-16095

  • DOI: https://doi.org/10.1074/jbc.M200493200
  • Primary Citation of Related Structures:  
    1KWT, 1KWU, 1KWV, 1KWW, 1KWX, 1KWY, 1KWZ, 1KX0, 1KX1, 1KZA, 1KZB, 1KZC, 1KZD, 1KZE

  • PubMed Abstract: 

    Mannose-binding proteins (MBPs) are C-type animal lectins that recognize high mannose oligosaccharides on pathogenic cell surfaces. MBPs bind to their carbohydrate ligands by forming a series of Ca(2+) coordination and hydrogen bonds with two hydroxyl groups equivalent to the 3- and 4-OH of mannose. In this work, the determinants of the orientation of sugars bound to rat serum and liver MBPs (MBP-A and MBP-C) have been systematically investigated. The crystal structures of MBP-A soaked with monosaccharides and disaccharides and also the structure of the MBP-A trimer cross-linked by a high mannose asparaginyl oligosaccharide reveal that monosaccharides or alpha1-6-linked mannose bind to MBP-A in one orientation, whereas alpha1-2- or alpha1-3-linked mannose binds in an orientation rotated 180 degrees around a local symmetry axis relating the 3- and 4-OH groups. In contrast, a similar set of ligands all bind to MBP-C in a single orientation. The mutation of MBP-A His(189) to its MBP-C equivalent, valine, causes Man alpha 1-3Man to bind in a mixture of orientations. These data combined with modeling indicate that the residue at this position influences the orientation of bound ligands in MBP. We propose that the control of binding orientation can influence the recognition of multivalent ligands. A lateral association of trimers in the cross-linked crystals may reflect interactions within higher oligomers of MBP-A that are stabilized by multivalent ligands.


  • Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MANNOSE-BINDING PROTEIN A
A, B, C, D, E
A, B, C, D, E, F
149Rattus norvegicusMutation(s): 0 
Gene Names: MBL1
UniProt
Find proteins for P19999 (Rattus norvegicus)
Explore P19999 
Go to UniProtKB:  P19999
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19999
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose
G, H
6N/A
Glycosylation Resources
GlyTouCan:  G80483PX
GlyCosmos:  G80483PX
GlyGen:  G80483PX
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download Ideal Coordinates CCD File 
L [auth B],
V [auth E]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
I [auth A]
J [auth A]
K [auth A]
AA [auth F],
BA [auth F],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth C],
Q [auth C],
R [auth C],
S [auth D],
T [auth D],
U [auth D],
W [auth E],
X [auth E],
Y [auth E],
Z [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.8α = 90
b = 255.56β = 119.6
c = 61.79γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary