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), 0.220 (DCC)
R-Value Work:
0.177 (Depositor), 0.190 (DCC)

wwPDB Validation 3D Report Full Report

This is version 1.0 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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibronectin	A	101	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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), 0.220 (DCC)
R-Value Work: 0.177 (Depositor), 0.190 (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

View Full Validation Report

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

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.