9IQK | pdb_00009iqk

SacM in complex with LC3

• PDB DOI: https://doi.org/10.2210/pdb9IQK/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Saccharothrix syringae
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-07-12 Released: 2025-07-16 
• Deposition Author(s): Zhang, B., Ge, H.M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.232 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Tandem Michael addition and Knoevenagel condensation catalyzed by NTF2-Like Enzymes as iminium catalysis

Liu, C.L., Zhang, B., Ge, H.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 30.6 kDa 
• Atom Count: 2,151 
• Modeled Residue Count: 245 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear transport factor 2 family protein	A, B	133	Saccharothrix syringae	Mutation(s): 0  Gene Names: EKG83_24495
UniProt
Find proteins for A0A5Q0H2K6 (Saccharothrix syringae) Explore A0A5Q0H2K6  Go to UniProtKB:  A0A5Q0H2K6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D9Z (Subject of Investigation/LOI)	C [auth A], D [auth B]	(2~{R},3~{R})-4-oxidanyl-3-propyl-2-[(3~{E},6~{S},7~{S},9~{E})-3,7,9-trimethyl-6,11-bis(oxidanyl)-2-oxidanylidene-undeca-3,9-dienyl]-2,3-dihydropyran-6-one C22 H34 O6 UCBTXUVTSVSRBB-MHZDCPSDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.232 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.25	α = 90
b = 52.25	β = 90
c = 202.839	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Zhang, B., Ge, H.M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22277051,81925033, 22193071

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release