1C39

STRUCTURE OF CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR BOUND TO PENTAMANNOSYL PHOSPHATE

• PDB DOI: https://doi.org/10.2210/pdb1C39/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bos taurus
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 1999-07-25 Released: 2000-01-14 
• Deposition Author(s): Olson, L.J., Zhang, J., Lee, Y.C., Dahms, N.M., Kim, J.J.-P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.246 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.55 kDa 
• Atom Count: 2,711 
• Modelled Residue Count: 304 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATION-DEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR	A, B	152	Bos taurus	Mutation(s): 4
UniProt
Find proteins for P11456 (Bos taurus) Explore P11456  Go to UniProtKB:  P11456

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
6-O-phosphono-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose	E, F	3		N/A
Glycosylation Resources
GlyTouCan:  G02301DT GlyCosmos:  G02301DT GlyGen:  G02301DT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	G [auth A], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.246 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.84	α = 90
b = 79.31	β = 100.33
c = 55.57	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-01-14 
Deposition Author(s): Olson, L.J., Zhang, J., Lee, Y.C., Dahms, N.M., Kim, J.J.-P.

Revision History  

• Version 1.0: 2000-01-14
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2018-03-14
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-08-09
  Changes: Data collection, Database references, Refinement description, Structure summary