4MA1

Unliganded 3 crystal structure of S25-26 Fab

• PDB DOI: https://doi.org/10.2210/pdb4MA1/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2013-08-15 Released: 2014-04-09 
• Deposition Author(s): Haji-Ghassemi, O., Evans, S.V.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.260 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 

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)

Biological Assembly 3  

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 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 147.23 kDa 
• Atom Count: 10,552 
• Modelled Residue Count: 1,309 
• Deposited Residue Count: 1,314 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S25-26 Fab (IgG1k) heavy chain	A [auth B], B [auth E], C [auth H]	219	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S25-26 Fab (IgG1k) light chain	D [auth C], E [auth F], F [auth L]	219	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth A]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G00395TQ GlyCosmos:  G00395TQ GlyGen:  G00395TQ

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth D]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42466VF GlyCosmos:  G42466VF GlyGen:  G42466VF

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth G]	9		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32704TW GlyCosmos:  G32704TW GlyGen:  G32704TW

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	J [auth B], K [auth H]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
K	L	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A [auth B], B [auth E], C [auth H]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.260 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 196.257	α = 90
b = 66.508	β = 113.46
c = 122.078	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-09 
Deposition Author(s): Haji-Ghassemi, O., Evans, S.V.

Revision History  

• Version 1.0: 2014-04-09
  Type: Initial release
  
• Version 1.1: 2014-06-11
  Changes: Database references
• Version 1.2: 2014-07-09
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 2.0: 2019-12-25
  Changes: Data collection, Derived calculations, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary