9YKB | pdb_00009ykb

The von Willebrand factor A domain of human capillary morphogenesis gene II, fused to the 1TEL crystallization chaperone, Ala-Val linker variant, expressed with SUMO tag.

PDB DOI: https://doi.org/10.2210/pdb9YKB/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-10-06 Released: 2025-10-22
Deposition Author(s): Gajjar, P., Samarawickrama, P., Pedroza Romo, M.J., Keliiliki, A., Litchfield, C., Callahan, M., Redd, N., Doukov, T., Lebedev, A., Moody, J.D.
Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.194 (Depositor), 0.194 (DCC)
R-Value Work:
0.179 (Depositor), 0.178 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9YKB

This is version 1.0 of the entry. See complete history.

Literature

1TEL Fusions Outperform 2TEL and 3TEL Fusions in Controlled Comparisons

Samarawickrama, P., Mead, D., Ludlow, K., Probst, R., Doukov, T., Moody, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 86.16 kDa
Atom Count: 6,220
Modeled Residue Count: 763
Deposited Residue Count: 771
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor ETV6,Anthrax toxin receptor 2	A, B [auth C], C [auth B]	257	Homo sapiens	Mutation(s): 6 Gene Names: ETV6, TEL, TEL1, ANTXR2, CMG2
UniProt & NIH Common Fund Data Resources
Find proteins for P41212 (Homo sapiens) Explore P41212 Go to UniProtKB: P41212
PHAROS: P41212 GTEx: ENSG00000139083
Find proteins for P58335 (Homo sapiens) Explore P58335 Go to UniProtKB: P58335
PHAROS: P58335 GTEx: ENSG00000163297
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P41212 P58335
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth B], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.194 (Depositor), 0.194 (DCC)
R-Value Work: 0.179 (Depositor), 0.178 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.745	α = 90
b = 163.745	β = 90
c = 54.246	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Samarawickrama, P.

Pedroza Romo, M.J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	1R15GM146209, 1R35GM155011

Revision History (Full details and data files)

Version 1.0: 2025-10-22
Type: Initial release

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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.