5L88

AFAMIN ANTIBODY FRAGMENT, N14 FAB, L1- GLYCOSILATED, CRYSTAL FORM I, non-parsimonious model

• PDB DOI: https://doi.org/10.2210/pdb5L88/pdb

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


• Deposited: 2016-06-07 Released: 2016-08-03 
• Deposition Author(s): Rupp, B., Naschberger, A.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.211 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.21 kDa 
• Atom Count: 3,847 
• Modelled Residue Count: 432 
• Deposited Residue Count: 435 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-afamin antibody N14, Fab fragment, heavy chain	A [auth H]	220	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-afamin antibody N14, Fab fragment, light chain	B [auth L]	215	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth A]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE8	G [auth H]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C16 H34 O9 GLZWNFNQMJAZGY-UHFFFAOYSA-N
1PE	O [auth L]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PG4	D [auth H], E [auth H], F [auth H], K [auth H]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	H, N [auth H], P [auth L], Q [auth L], R [auth L]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	I [auth H], J [auth H], L [auth H]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
K	M [auth H]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.211 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.782	α = 90
b = 69.249	β = 90
c = 87.803	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data collection
autoPROC	data scaling
XDS	data reduction
SCALA	data scaling
BALBES	phasing
Coot	model building
WARP	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-08-03 
Deposition Author(s): Rupp, B., Naschberger, A.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P28395-B26

Revision History  

• Version 1.0: 2016-08-03
  Type: Initial release
  
• Version 1.1: 2016-11-16
  Changes: Data collection
• Version 1.2: 2016-12-07
  Changes: Database references
• Version 1.3: 2016-12-21
  Changes: Database references
• Version 1.4: 2017-09-06
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary