1RDN

MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH ALPHA-METHYL-D-N-ACETYLGLUCOSAMINIDE

• PDB DOI: https://doi.org/10.2210/pdb1RDN/pdb

• Classification: LECTIN
• Organism(s): Rattus rattus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1995-09-05 Released: 1996-03-08 
• Deposition Author(s): Ng, K.K.-S., Drickamer, K., Weis, W.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 

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: 25.99 kDa 
• Atom Count: 2,080 
• Modelled Residue Count: 223 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MANNOSE-BINDING PROTEIN-C	A [auth 1], B [auth 2]	113	Rattus rattus	Mutation(s): 0
UniProt
Find proteins for P08661 (Rattus norvegicus) Explore P08661  Go to UniProtKB:  P08661

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDG	C [auth 1], G [auth 2]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
CA	D [auth 1], E [auth 1], H [auth 2], I [auth 2]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth 1]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
NDG	Binding MOAD:  1RDN	Ki: 1.44e+7 (nM) from 1 assay(s)
MAG	PDBBind:  1RDN	Ki: 1.44e+7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.6	α = 90
b = 75.2	β = 90
c = 57.4	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: 1996-03-08 
Deposition Author(s): Ng, K.K.-S., Drickamer, K., Weis, W.I.

Revision History  

• Version 1.0: 1996-03-08
  Type: Initial release
  
• Version 1.1: 2008-03-03
  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: Atomic model, Data collection, Derived calculations, Structure summary