8ZCL | pdb_00008zcl

Ambient Temperature Crystal Structure of Fc Fragment of Human IgG1 from Biosimilar VEGF-Trap

PDB DOI: https://doi.org/10.2210/pdb8ZCL/pdb

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

Deposited: 2024-04-30 Released: 2024-05-08
Deposition Author(s): Destan, E., DeMirci, H.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.236 (Depositor), 0.230 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF-Trap

Destan, E., Turkut, E., Aldeniz, A., Kang, J., Tosha, T., Yabashi, M., Yilmaz, B., Timucin, C., Matsuura, H., Kawano, Y., Cinkaya, I., Demirci, H.

(2025) Small Struct

DOI: https://doi.org/10.1002/sstr.202400680

Macromolecule Content

Total Structure Weight: 50.15 kDa
Atom Count: 3,615
Modeled Residue Count: 413
Deposited Residue Count: 416
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin gamma-1 heavy chain	A, B	208	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5 Go to UniProtKB: P0DOX5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DOX5
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-3)]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	C	9		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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	D	7		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G45889JQ GlyCosmos: G45889JQ GlyGen: G45889JQ

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.236 (Depositor), 0.230 (DCC)
R-Value Work: 0.179 (Depositor), 0.180 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.47	α = 90
b = 79.99	β = 90
c = 143.19	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Turkey	119C132

Revision History (Full details and data files)

Version 1.0: 2024-05-08
Type: Initial release
Version 1.1: 2024-10-30
Changes: Structure summary
Version 1.2: 2025-05-21
Changes: Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.