5MTH

Structure of DC8E8 Fab at pH 6.5 crystallized in spacegroup P21

• PDB DOI: https://doi.org/10.2210/pdb5MTH/pdb

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


• Deposited: 2017-01-09 Released: 2018-05-02 
• Deposition Author(s): Skrabana, R., Novak, M., Cehlar, O., Kontsekova, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.235 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

Structure of DC8E8 Fab at pH 6.5 crystallized in spacegroup P21

Skrabana, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 97.82 kDa 
• Atom Count: 7,524 
• Modelled Residue Count: 879 
• Deposited Residue Count: 880 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody Fab heavy chain	A [auth H], C [auth A]	221	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody Fab light chain	B [auth L], D [auth B]	219	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	E [auth C], F [auth D], G [auth E], H [auth F]	2		N/A
Glycosylation Resources
GlyTouCan:  G92130SN GlyCosmos:  G92130SN

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	I [auth H], J [auth H], K [auth A], L [auth A], M [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006	E [auth C], F [auth D], G [auth E], H [auth F]	trehalose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.235 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.45	α = 90
b = 111.77	β = 90.56
c = 95.64	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Skrabana, R., Novak, M., Cehlar, O., Kontsekova, E.

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2019-08-14
  Changes: Data collection
• Version 2.0: 2020-03-11
  Changes: Atomic model, Data collection, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 3.2: 2024-11-06
  Changes: Structure summary