1OQO | pdb_00001oqo

Complex between G0 version of an Fc bound to a minimized version of Protein A called Mini-Z

PDB DOI: https://doi.org/10.2210/pdb1OQO/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, synthetic construct
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2003-03-10 Released: 2003-03-20
Deposition Author(s): Raju, T.S., Mulkerrin, M.G., Parker, M., De Vos, A.M., Gazzano-Santoro, H., Totpal, K., Ultsch, M.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.286 (Depositor), 0.277 (DCC)
R-Value Work:
0.216 (Depositor), 0.211 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 3.2 of the entry. See complete history.

Literature

Impact of Fc Glycans on The Effector Functions Vary with the Antibody mechanism of Action

Raju, T.S., Mulkerrin, M.G., Parker, M., De Vos, A.M., Gazzano-Santoro, H., Totpal, K., Ultsch, M.H.

To be published.

Macromolecule Content

Total Structure Weight: 59.26 kDa
Atom Count: 4,246
Modeled Residue Count: 484
Deposited Residue Count: 492
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
immunoglobulin gamma-1 heavy chain constant region	A, C [auth B]	212	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857 Go to UniProtKB: P01857
PHAROS: P01857 GTEx: ENSG00000211896
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01857
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain C [auth B]	Go to GlyGen: P01857-2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Minimized version of Protein A (Z34C)	B [auth C], D	34	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E	8		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G59451NL GlyCosmos: G59451NL GlyGen: G59451NL

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F	8		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G50842MS GlyCosmos: G50842MS GlyGen: G50842MS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.286 (Depositor), 0.277 (DCC)
R-Value Work: 0.216 (Depositor), 0.211 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.782	α = 90
b = 126.413	β = 90
c = 54.743	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-03-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-03-20
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 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 3.0: 2020-12-16
Changes: Advisory, Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary
Version 3.1: 2023-08-16
Changes: Data collection, Database references, Refinement description
Version 3.2: 2024-10-30
Changes: Structure summary