7YPL | pdb_00007ypl

Crystal structure of fibronectin type III domain variant, a VEGFR2-specific antagonist

PDB DOI: https://doi.org/10.2210/pdb7YPL/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-08-03 Released: 2023-08-16
Deposition Author(s): Chang, Y.T., Chen, C.Y., Chuang, W.J.
Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.213 (Depositor), 0.224 (DCC)
R-Value Work:
0.177 (Depositor), 0.191 (DCC)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

A Novel Disulfide Bond Engineering of Fibronectin Type III Domain Enhances Thermostability and Solubility of VEGFR2-Specific Antagonist

Chang, Y.S., Katte, R.H., Lin, C.C., Chang, Y.T., Chen, C.Y., Chuang, W.J.

To be published.

Macromolecule Content

Total Structure Weight: 11.5 kDa
Atom Count: 877
Modeled Residue Count: 100
Deposited Residue Count: 101
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibronectin	A	101	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.213 (Depositor), 0.224 (DCC)
R-Value Work: 0.177 (Depositor), 0.191 (DCC)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.791	α = 90
b = 68.791	β = 90
c = 68.799	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-08-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History (Full details and data files)

Version 1.0: 2023-08-16
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.