6PLH

FAB fragment complexed with C-mannosylated tryptophan peptide

• PDB DOI: https://doi.org/10.2210/pdb6PLH/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2019-06-30 Released: 2020-07-08 
• Deposition Author(s): John, A., Jarva, M.A., Goddard-Borger, E.D.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.221 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 52.6 kDa 
• Atom Count: 3,855 
• Modelled Residue Count: 446 
• Deposited Residue Count: 479 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 5G12 light chain	A	219	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 5G12 heavy chain	B	223	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-21 receptor	C	37	Homo sapiens	Mutation(s): 0  Gene Names: IL21R, NILR, UNQ3121/PRO10273
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HBE5 (Homo sapiens) Explore Q9HBE5  Go to UniProtKB:  Q9HBE5
PHAROS:  Q9HBE5 GTEx:  ENSG00000103522

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN (Subject of Investigation/LOI)	E [auth C]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	B	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.221 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.232	α = 90
b = 89.892	β = 95.94
c = 59.317	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): John, A., Jarva, M.A., Goddard-Borger, E.D.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT1139546

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.3: 2021-02-17
  Changes: Database references
• Version 1.4: 2021-03-31
  Changes: Database references
• Version 1.5: 2023-10-11
  Changes: Data collection, Database references, Refinement description