9IQL | pdb_00009iql

SacM in complex with L6S

PDB DOI: https://doi.org/10.2210/pdb9IQL/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.225 (Depositor), 0.227 (DCC)
R-Value Work:
0.209 (Depositor), 0.210 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural and mechanistic insights into iminium-catalysed macrocyclization by nuclear transport factor 2-like enzymes

Liu, C.L., Zhang, B., Ge, H.M.

(2026) Nat Synth

DOI: https://doi.org/10.1038/s44160-025-00989-z

Macromolecule Content

Total Structure Weight: 30.93 kDa
Atom Count: 2,162
Modeled Residue Count: 246
Deposited Residue Count: 266
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5Q0H2K6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D90 (Subject of Investigation/LOI) Query on A1D90 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	(5~{R},6~{R})-6-[(~{E})-5-[(2~{S},3~{S},5~{S})-5-(2-hydroxyethyl)-3,5-dimethyl-oxolan-2-yl]-3-methyl-2-oxidanylidene-pent-3-enyl]-5-propyl-oxane-2,4-dione C₂₂ H₃₄ O₆ MVJVJKSGEMISOL-KHRHQXNTSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]