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)

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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

Literature

Computational design of verteporfin binding protein

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

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

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
P15	D [auth A]	2,5,8,11,14,17-HEXAOXANONADECAN-19-OL C13 H28 O7 FHHGCKHKTAJLOM-UHFFFAOYSA-N
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Tang, X., Li, Y.H., Xu, Y.L., Kou, L.Y., Ji, P.F.

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

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release