5JOP

Crystal structure of anti-glycan antibody Fab14.22 in complex with Streptococcus pneumoniae serotype 14 tetrasaccharide at 1.75 A

PDB DOI: https://doi.org/10.2210/pdb5JOP/pdb

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

Deposited: 2016-05-02 Released: 2017-03-22
Deposition Author(s): Sarkar, A., Irimia, A., Teyton, L., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.200
R-Value Work: 0.165
R-Value Observed: 0.167

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 105.89 kDa
Atom Count: 8,094
Modelled Residue Count: 855
Deposited Residue Count: 936
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 14.22 light chain	A [auth D], C [auth L]	219	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab14.22 heavy chain	B [auth E], D [auth H]	249	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose-(1-6)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth A], F [auth B]	4		N/A	Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]
Glycosylation Resources
GlyTouCan: G09494DM GlyCosmos: G09494DM GlyGen: G09494DM

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain G [auth D] SDF format, chain J [auth E] SDF format, chain R [auth L] SDF format, chain S [auth L] SDF format, chain T [auth L] MOL2 format, chain AA [auth H] MOL2 format, chain G [auth D] MOL2 format, chain J [auth E] MOL2 format, chain R [auth L] MOL2 format, chain S [auth L] MOL2 format, chain T [auth L]	AA [auth H] G [auth D] J [auth E] R [auth L] S [auth L] AA [auth H], G [auth D], J [auth E], R [auth L], S [auth L], T [auth L]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth H] Focus chain G [auth D] Focus chain J [auth E] Focus chain R [auth L] Focus chain S [auth L] Focus chain T [auth L] Interactions & Density Focus chain AA [auth H] Focus chain G [auth D] Focus chain J [auth E] Focus chain R [auth L] Focus chain S [auth L] Focus chain T [auth L]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain H [auth D] SDF format, chain I [auth D] SDF format, chain K [auth E] SDF format, chain L [auth E] SDF format, chain M [auth E] SDF format, chain N [auth E] SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain Q [auth E] SDF format, chain U [auth L] SDF format, chain V [auth L] SDF format, chain W [auth L] SDF format, chain X [auth L] SDF format, chain Y [auth L] SDF format, chain Z [auth L] MOL2 format, chain BA [auth H] MOL2 format, chain H [auth D] MOL2 format, chain I [auth D] MOL2 format, chain K [auth E] MOL2 format, chain L [auth E] MOL2 format, chain M [auth E] MOL2 format, chain N [auth E] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain U [auth L] MOL2 format, chain V [auth L] MOL2 format, chain W [auth L] MOL2 format, chain X [auth L] MOL2 format, chain Y [auth L] MOL2 format, chain Z [auth L]	BA [auth H] H [auth D] I [auth D] K [auth E] L [auth E] BA [auth H], H [auth D], I [auth D], K [auth E], L [auth E], M [auth E], N [auth E], O [auth E], P [auth E], Q [auth E], U [auth L], V [auth L], W [auth L], X [auth L], Y [auth L], Z [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain H [auth D] Focus chain I [auth D] Focus chain K [auth E] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth E] Focus chain U [auth L] Focus chain V [auth L] Focus chain W [auth L] Focus chain X [auth L] Focus chain Y [auth L] Focus chain Z [auth L] Interactions & Density Focus chain BA [auth H] Focus chain H [auth D] Focus chain I [auth D] Focus chain K [auth E] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth E] Focus chain U [auth L] Focus chain V [auth L] Focus chain W [auth L] Focus chain X [auth L] Focus chain Y [auth L] Focus chain Z [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.200
R-Value Work: 0.165
R-Value Observed: 0.167
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.267	α = 90
b = 74.74	β = 100.55
c = 120.304	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-03-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-03-22
Type: Initial release
Version 1.1: 2017-04-12
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary