8GQP | pdb_00008gqp

Complex of D-protein binder D-19437 and L-target L-Pep-1

• PDB DOI: https://doi.org/10.2210/pdb8GQP/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): artificial sequences
• Mutation(s): No 


• Deposited: 2022-08-30 Released: 2023-09-13 
• Deposition Author(s): Liang, M.F., Li, S.C., Wang, T.Y., Liu, L., Lu, P.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.226 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Accurate de novo design of heterochiral protein-protein interactions

Sun, K., Li, S., Zheng, B., Zhu, Y., Wang, T., Liang, M., Yao, Y., Zhang, K., Zhang, J., Li, H., Han, D., Zheng, J., Coventry, B., Cao, L., Baker, D., Liu, L., Lu, P.

(2024) Cell Res 

• DOI: https://doi.org/10.1038/s41422-024-01014-2

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, isothermal titration calorimetry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.5 kDa 
• Atom Count: 1,415 
• Modeled Residue Count: 161 
• Deposited Residue Count: 164 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-binder	A, C	62	artificial sequences	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L-pep1	B, D	20	artificial sequences	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.226 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.395	α = 90
b = 82.282	β = 90
c = 35.323	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Liang, M.F., Li, S.C., Wang, T.Y., Liu, L., Lu, P.L.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22137005
Ministry of Science and Technology (MoST, China)	China	2020YFA0909200

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release
  
• Version 1.1: 2024-09-25
  Changes: Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary