12KI | pdb_000012ki

Designed pentameric proton channel LLQL I13S

• PDB DOI: https://doi.org/10.2210/pdb12KI/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2026-04-09 Released: 2026-05-06 
• Deposition Author(s): Jacob, N.P., Kratochvil, H.T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.242 (DCC) 

Starting Model: experimental

Literature

Engineered Channel Asymmetry Extends Hydrogen-Bonding Networks for Proton Conduction

Jacob, N.P., Silverman, V.T., Prida, G., Kratochvil, H.T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

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

Macromolecule Content 

• Total Structure Weight: 31 kDa 
• Atom Count: 2,173 
• Modeled Residue Count: 257 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proton channel LLQL I13S	A, B, C, D, E, F, G, H, I, J	26	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	K [auth B]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
PEG	L [auth B], O [auth I], P [auth J]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	M [auth C], N [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.242 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.181	α = 90
b = 85.409	β = 90
c = 87.192	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-06 
Deposition Author(s): Jacob, N.P., Kratochvil, H.T.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R00GM138753

Revision History  

• Version 1.0: 2026-05-06
  Type: Initial release