8A1A | pdb_00008a1a

Structure of a leucinostatin derivative determined by host lattice display : L1F11V1 construct

• PDB DOI: https://doi.org/10.2210/pdb8A1A/pdb

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


• Deposited: 2022-06-01 Released: 2022-12-07 
• Deposition Author(s): Mittl, P.R.E.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.185 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Structure of a hydrophobic leucinostatin derivative determined by host lattice display.

Kiss, C., Gall, F.M., Dreier, B., Adams, M., Riedl, R., Pluckthun, A., Mittl, P.R.E.

(2022) Acta Crystallogr D Struct Biol 78: 1439-1450

• PubMed: 36458615 
• DOI: https://doi.org/10.1107/S2059798322010762
• Primary Citation Related Structures: 
  8A19, 8A1A


• PubMed Abstract: 
  

  Peptides comprising many hydrophobic amino acids are almost insoluble under physiological buffer conditions, which complicates their structural analysis. To investigate the three-dimensional structure of the hydrophobic leucinostatin derivative ZHAWOC6027, the previously developed host lattice display technology was applied. Two designed ankyrin-repeat proteins (DARPins) recognizing a biotinylated ZHAWOC6027 derivative were selected from a diverse library by ribosome display under aqueous buffer conditions. ZHAWOC6027 was immobilized by means of the DARPin in the host lattice and the structure of the complex was determined by X-ray diffraction. ZHAWOC6027 adopts a distorted α-helical conformation. Comparison with the structures of related compounds that have been determined in organic solvents reveals elevated flexibility of the termini, which might be functionally important.

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Organizational Affiliation: 
• Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
Institute of Chemistry and Biotechnology, Competence Center for Drug discovery, ZHAW Zurich University of Applied Science, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland.
Bacoba AG, Elisabethenstrasse 15, 4051 Basel, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 149.24 kDa 
• Atom Count: 12,109 
• Modeled Residue Count: 1,356 
• Deposited Residue Count: 1,358 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L1F11v1	A	1,347	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
6-(2-methoxyethoxy)-11,15-dimethyl-8-oxa-2,11,15,19,21,23-hexazatetracyclo[15.6.1.13,7.020,24]pentacosa-1(23),3(25),4,6,17,20(24),21-heptaen-10-one	B	11	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	K [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
MPD	G [auth A], H [auth A], I [auth A], J [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
MN	C [auth A], D [auth A], E [auth A], F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	L [auth A], M [auth A], N [auth A], O [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AIB	B	L-PEPTIDE LINKING	C4 H9 N O2		ALA
BAL	B	PEPTIDE-LIKE	C3 H7 N O2		--
HPE	B	L-PEPTIDE LINKING	C10 H13 N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.185 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M38A1A

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 191.866	α = 90
b = 191.866	β = 90
c = 122.409	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
autoPROC	data scaling
BUSTER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-07 
Deposition Author(s): Mittl, P.R.E.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-12-07
  Type: Initial release
  
• Version 1.1: 2022-12-14
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description