7ARN | pdb_00007arn

Crystal Structure of the Fab Fragment of a Glycosylated Lymphoma Antibody

PDB DOI: https://doi.org/10.2210/pdb7ARN/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2020-10-25 Released: 2021-11-03
Deposition Author(s): Pryce, R., Allen, J.D., Watanabe, Y., Crispin, M., Bowden, T.A.
Funding Organization(s): Bloodwise, Cancer Research UK, Medical Research Council (MRC, United Kingdom), Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.232 (Depositor), 0.231 (DCC)
R-Value Work:
0.195 (Depositor), 0.196 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of the Fab Fragment of a Glycosylated Lymphoma Antibody

Allen, J.D., Pryce, R., Watanabe, Y., Crispin, M., Bowden, T.A.

To be published.

Macromolecule Content

Total Structure Weight: 56.18 kDa
Atom Count: 3,823
Modeled Residue Count: 438
Deposited Residue Count: 509
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fab Fragment Heavy Chain	A [auth H]	262	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Fab Fragment Light Chain	B [auth L]	247	Homo sapiens	Mutation(s): 0

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth A]	3		N-Glycosylation	Interactions Focus chain C [auth A]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	5		N-Glycosylation	Interactions Focus chain D [auth B]
Glycosylation Resources
GlyTouCan: G94626GC GlyCosmos: G94626GC GlyGen: G94626GC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth H] SDF format, chain G [auth L] SDF format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain G [auth L] MOL2 format, chain E [auth H] mmCIF format, chain F [auth H] mmCIF format, chain G [auth L] mmCIF format, chain E [auth H]	E [auth H], F [auth H], G [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.232 (Depositor), 0.231 (DCC)
R-Value Work: 0.195 (Depositor), 0.196 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.55	α = 90
b = 60.58	β = 111.91
c = 82.45	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-11-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Bloodwise	United Kingdom	18009
Cancer Research UK	United Kingdom	C42023/A29370
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/L009528/1 and MR/S007555/1
Wellcome Trust	United Kingdom	203141/Z/16/Z