3DUR

Crystal structure of SAG173-04

• PDB DOI: https://doi.org/10.2210/pdb3DUR/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-17 Released: 2008-12-02 
• Deposition Author(s): Brooks, C.L., Blackler, R.J., Gerstenbruch, S., Kosma, P., Muller-Loennies, S., Brade, H., Evans, S.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.247 
• R-Value Work: 0.178 
• R-Value Observed: 0.182 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.4 kDa 
• Atom Count: 4,132 
• Modelled Residue Count: 466 
• Deposited Residue Count: 466 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody Fv fragment SAG173-04	A, C	112	Mus musculus	Mutation(s): 0
UniProt
Find proteins for A2N494 (Mus musculus) Explore A2N494  Go to UniProtKB:  A2N494

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig-like protein	B, D	121	Mus musculus	Mutation(s): 0
UniProt
Find proteins for A2NU21 (Mus musculus) Explore A2NU21  Go to UniProtKB:  A2NU21

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KDO	E [auth A], I [auth D]	3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid C8 H14 O8 NNLZBVFSCVTSLA-HXUQBWEZSA-N
PG4	G [auth B], J [auth D]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
MG	F [auth A], H [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.247 
• R-Value Work: 0.178 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.76	α = 90
b = 72.19	β = 90
c = 85.13	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-02 
Deposition Author(s): Brooks, C.L., Blackler, R.J., Gerstenbruch, S., Kosma, P., Muller-Loennies, S., Brade, H., Evans, S.V.

Revision History  

• Version 1.0: 2008-12-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary