6C5I

Unliganded S25-5 Fab

• PDB DOI: https://doi.org/10.2210/pdb6C5I/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2018-01-16 Released: 2019-01-09 
• Deposition Author(s): Evans, S.V., Haji-Ghassemi, O.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.231 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

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 Evidence: homology

Macromolecule Content

• Total Structure Weight: 48.31 kDa 
• Atom Count: 3,713 
• Modelled Residue Count: 435 
• Deposited Residue Count: 437 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab IgG1 Heavy Chain	A [auth H]	218	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q99LC4 (Mus musculus) Explore Q99LC4  Go to UniProtKB:  Q99LC4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab IgG1 (kappa) Light Chain	B [auth L]	219	Mus musculus	Mutation(s): 0
UniProt
Find proteins for A0A0F7R5U8 (Mus musculus) Explore A0A0F7R5U8  Go to UniProtKB:  A0A0F7R5U8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG0	G [auth L], H [auth L]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
NI	E [auth L], F [auth L]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	D [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.231 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.635	α = 90
b = 72.877	β = 90
c = 109.015	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-09 
Deposition Author(s): Evans, S.V., Haji-Ghassemi, O.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	Discovery Grant 171356-2013

Revision History  

• Version 1.0: 2019-01-09
  Type: Initial release
  
• Version 1.1: 2019-02-27
  Changes: Data collection, Database references
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary