9VVN | pdb_00009vvn

Crystal structure of computationally designed protein VTP-4

PDB DOI: https://doi.org/10.2210/pdb9VVN/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-07-16 Released: 2025-08-13
Deposition Author(s): Tang, X., Li, Y.H., Xu, Y.L., Kou, L.Y., Ji, P.F.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.255 (Depositor), 0.265 (DCC)
R-Value Work:
0.207 (Depositor), 0.219 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9VVN

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

Literature

Computational design of verteporfin binding protein

Tang, X., Li, Y.H., Xu, Y.L., Kou, L.Y., Ji, P.F.

To be published.

Macromolecule Content

Total Structure Weight: 20.78 kDa
Atom Count: 1,509
Modeled Residue Count: 167
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VTP-4	A	182	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P15 Query on P15 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2,5,8,11,14,17-HEXAOXANONADECAN-19-OL C₁₃ H₂₈ O₇ FHHGCKHKTAJLOM-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.255 (Depositor), 0.265 (DCC)
R-Value Work: 0.207 (Depositor), 0.219 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.606	α = 90
b = 58.488	β = 90
c = 83.828	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22377107

Revision History (Full details and data files)

Version 1.0: 2025-08-13
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.