7YH8 | pdb_00007yh8

Crystal structure of a heterochiral protein complex

• PDB DOI: https://doi.org/10.2210/pdb7YH8/pdb

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


• Deposited: 2022-07-13 Released: 2023-07-19 
• Deposition Author(s): Liang, M., Li, S., Wang, T., Liu, L., Lu, P.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.250 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.205 (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 2  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.37 kDa 
• Atom Count: 1,440 
• Modeled Residue Count: 162 
• Deposited Residue Count: 162 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-19437	A, C	62	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-Pep-1	B, D	19	artificial sequences	Mutation(s): 0

Small Molecules

Modified Residues  12 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAL	B, D	D-PEPTIDE LINKING	C3 H7 N O2		--
DAR	B, D	D-PEPTIDE LINKING	C6 H15 N4 O2		--
DAS	B, D	D-PEPTIDE LINKING	C4 H7 N O4		--
DGL	B, D	D-PEPTIDE LINKING	C5 H9 N O4		--
DHI	B, D	D-PEPTIDE LINKING	C6 H10 N3 O2		--
DIL	B, D	D-PEPTIDE LINKING	C6 H13 N O2		--
DLE	B, D	D-PEPTIDE LINKING	C6 H13 N O2		--
DLY	B, D	D-PEPTIDE LINKING	C6 H14 N2 O2		--
DPN	B, D	D-PEPTIDE LINKING	C9 H11 N O2		--
DTH	B, D	D-PEPTIDE LINKING	C4 H9 N O3		--
DTR	B, D	D-PEPTIDE LINKING	C11 H12 N2 O2		--
DTY	B, D	D-PEPTIDE LINKING	C9 H11 N O3		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.250 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.064	α = 90
b = 81.922	β = 90
c = 35.722	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
Coot	model building
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-19 
Deposition Author(s): Liang, M., Li, S., Wang, T., Liu, L., Lu, P.

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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: 2023-07-19
  Type: Initial release
  
• Version 1.1: 2024-09-25
  Changes: Data collection, Database references
• Version 1.2: 2024-11-13
  Changes: Structure summary