1S3K
Crystal Structure of a Humanized Fab (hu3S193) in Complex with the Lewis Y Tetrasaccharide
- PDB DOI: https://doi.org/10.2210/pdb1S3K/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Mus musculus
- Expression System: Mus musculus
- Mutation(s): No 
- Deposited: 2004-01-13 Released: 2004-07-13 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.238 
- R-Value Work: 0.203 
- R-Value Observed: 0.203 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
HU3S193 Fab fragment, light chain | A [auth L] | 219 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
HU3S193 Fab fragment, heavy chain | B [auth H] | 222 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose | C [auth A] | 4 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G82236PZ GlyCosmos:  G82236PZ GlyGen:  G82236PZ |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
GOL Query on GOL | D [auth L] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900124 Query on PRD_900124 | C [auth A] | Lewis Y antigen, alpha anomer | Oligosaccharide / Antigen |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.238 
- R-Value Work: 0.203 
- R-Value Observed: 0.203 
- Space Group: P 31
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 71.758 | α = 90 |
b = 71.758 | β = 90 |
c = 90.142 | γ = 120 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
CNS | refinement |
Entry History 
Deposition Data
- Released Date: 2004-07-13  Deposition Author(s): Ramsland, P.A., Farrugia, W., Bradford, T.M., Hogarth, P.M., Scott, A.M.
Revision History (Full details and data files)
- Version 1.0: 2004-07-13
Type: Initial release - Version 1.1: 2008-04-29
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2020-01-01
Changes: Data collection, Derived calculations, Source and taxonomy - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary