11IZ | pdb_000011iz

Crystal structure of HSC-HSC-AMS bound DesD, the desferrioxamine synthetase from the Streptomyces griseoflavus ferrimycin biosynthetic pathway

PDB DOI: https://doi.org/10.2210/pdb11IZ/pdb

Classification: LIGASE
Organism(s): Streptomyces griseoflavus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-02-26 Released: 2026-08-26
Deposition Author(s): Patel, K.D., Gulick, A.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free:
0.213 (Depositor), 0.214 (DCC)
R-Value Work:
0.175 (Depositor), 0.176 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Modular Inhibitor Approach to Map the Catalytic Trajectory of an Iterative Siderophore Synthetase, DesD.

Merrick, C.E., Patel, K.D., Kalita, P., Gulati, N., Gulick, A.M., Wencewicz, T.A.

(2026) ACS Bio Med Chem Au 6: 393-409

PubMed: 42630954 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsbiomedchemau.6c00078
Primary Citation Related Structures:
11IZ

PubMed Abstract:
Under iron limiting conditions, bacteria biosynthesize and secrete small molecule iron chelators, siderophores, to scavenge this essential metal. Siderophores are biosynthesized by nonribosomal peptide synthetases (NRPS) or NRPS independent siderophore (NIS) synthetases, the latter of which are significantly less studied. Streptomyces spp . utilizes an iterative NIS synthetase, DesD, to produce desferrioxamine type siderophores through dimerization, trimerization, and (in some cases) macrocyclization of monomers such as N ¹-hydroxy- N ¹-succinyl cadaverine (HSC) and N ¹-hydroxy- N ¹-acetyl cadaverine (HAC). Prior work has utilized an acyl-sulfamoyl adenosine (AMS) inhibitor of monomeric HSC (HSC-AMS) to interrogate the initial adenylation reaction of HSC. However, much is still unknown about how the enzyme active site accommodates substrates of varying sizes during further oligomerization reactions. To answer this question, AMS analogs of the monomer (HSC-AMS), dimer (HSC-HSC-AMS), and trimer (HSC-HSC-HSC-AMS) were chemically synthesized. Biochemical results from in vitro DesD reactions, IC ₅₀ assays, and isothermal titration calorimetry along with structural studies conducted via cocrystallization inform an updated mechanistic model for the iterative DesD catalytic cycle. The acyl adenylate motif in the growing substrate chain drives tight binding in the enzyme active site while the N-terminal HSC units dynamically sample conformations en route to terminating macrocyclization of the HSC-HSC-HSC trimer.

Organizational Affiliation

Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States.

Macromolecule Content

Total Structure Weight: 353.23 kDa
Atom Count: 24,914
Modeled Residue Count: 2,959
Deposited Residue Count: 3,060
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DesD	A [auth B], B [auth A], C [auth D], D [auth E], E [auth C]	612	Streptomyces griseoflavus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1C9F (Subject of Investigation/LOI) Query on A1C9F Download:Ideal Coordinates CCD File SDF format, chain XA [auth D] SDF format, chain NB [auth C] SDF format, chain N [auth B] SDF format, chain KA [auth A] SDF format, chain HB [auth E] MOL2 format, chain XA [auth D] MOL2 format, chain NB [auth C] MOL2 format, chain N [auth B] MOL2 format, chain KA [auth A] MOL2 format, chain HB [auth E] mmCIF format, chain XA [auth D] mmCIF format, chain NB [auth C] mmCIF format, chain N [auth B] mmCIF format, chain KA [auth A] mmCIF format, chain HB [auth E]	HB [auth E], KA [auth A], N [auth B], NB [auth C], XA [auth D]	5'-O-({4-[(5-{4-[(5-aminopentyl)(hydroxy)amino]-4-oxobutanamido}pentyl)(hydroxy)amino]-4-oxobutanoyl}sulfamoyl)adenosine C₂₈ H₄₆ N₁₀ O₁₂ S DTAWWDRDFOIVCY-JYQADIQDSA-N		Interactions Focus chain HB [auth E] Focus chain KA [auth A] Focus chain N [auth B] Focus chain NB [auth C] Focus chain XA [auth D] Interactions & Density Focus chain HB [auth E] Focus chain KA [auth A] Focus chain N [auth B] Focus chain NB [auth C] Focus chain XA [auth D]
DPO Query on DPO Download:Ideal Coordinates CCD File SDF format, chain YA [auth D] SDF format, chain OB [auth C] SDF format, chain O [auth B] SDF format, chain LA [auth A] SDF format, chain IB [auth E] MOL2 format, chain YA [auth D] MOL2 format, chain OB [auth C] MOL2 format, chain O [auth B] MOL2 format, chain LA [auth A] MOL2 format, chain IB [auth E] mmCIF format, chain YA [auth D] mmCIF format, chain OB [auth C] mmCIF format, chain O [auth B] mmCIF format, chain LA [auth A] mmCIF format, chain IB [auth E]	IB [auth E], LA [auth A], O [auth B], OB [auth C], YA [auth D]	DIPHOSPHATE O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-J		Interactions Focus chain IB [auth E] Focus chain LA [auth A] Focus chain O [auth B] Focus chain OB [auth C] Focus chain YA [auth D] Interactions & Density Focus chain IB [auth E] Focus chain LA [auth A] Focus chain O [auth B] Focus chain OB [auth C] Focus chain YA [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain VB [auth C] SDF format, chain UB [auth C] SDF format, chain U [auth B] SDF format, chain TB [auth C] SDF format, chain T [auth B] SDF format, chain SB [auth C] SDF format, chain S [auth B] SDF format, chain RB [auth C] SDF format, chain R [auth B] SDF format, chain QA [auth A] SDF format, chain PA [auth A] SDF format, chain OA [auth A] SDF format, chain FB [auth D] SDF format, chain EB [auth D] SDF format, chain DB [auth D] SDF format, chain CB [auth D] SDF format, chain BB [auth D] MOL2 format, chain VB [auth C] MOL2 format, chain UB [auth C] MOL2 format, chain U [auth B] MOL2 format, chain TB [auth C] MOL2 format, chain T [auth B] MOL2 format, chain SB [auth C] MOL2 format, chain S [auth B] MOL2 format, chain RB [auth C] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain FB [auth D] MOL2 format, chain EB [auth D] MOL2 format, chain DB [auth D] MOL2 format, chain CB [auth D] MOL2 format, chain BB [auth D] mmCIF format, chain VB [auth C] mmCIF format, chain UB [auth C] mmCIF format, chain U [auth B] mmCIF format, chain TB [auth C] mmCIF format, chain T [auth B] mmCIF format, chain SB [auth C] mmCIF format, chain S [auth B] mmCIF format, chain RB [auth C] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain FB [auth D] mmCIF format, chain EB [auth D] mmCIF format, chain DB [auth D] mmCIF format, chain CB [auth D] mmCIF format, chain BB [auth D]	BB [auth D] CB [auth D] DB [auth D] EB [auth D] FB [auth D] BB [auth D], CB [auth D], DB [auth D], EB [auth D], FB [auth D], OA [auth A], PA [auth A], QA [auth A], R [auth B], RB [auth C], S [auth B], SB [auth C], T [auth B], TB [auth C], U [auth B], UB [auth C], VB [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain R [auth B] Focus chain RB [auth C] Focus chain S [auth B] Focus chain SB [auth C] Focus chain T [auth B] Focus chain TB [auth C] Focus chain U [auth B] Focus chain UB [auth C] Focus chain VB [auth C] Interactions & Density Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain R [auth B] Focus chain RB [auth C] Focus chain S [auth B] Focus chain SB [auth C] Focus chain T [auth B] Focus chain TB [auth C] Focus chain U [auth B] Focus chain UB [auth C] Focus chain VB [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain WA [auth D] SDF format, chain W [auth A] SDF format, chain VA [auth D] SDF format, chain V [auth A] SDF format, chain UA [auth D] SDF format, chain TA [auth D] SDF format, chain SA [auth D] SDF format, chain RA [auth D] SDF format, chain MB [auth C] SDF format, chain M [auth B] SDF format, chain LB [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain JA [auth A] SDF format, chain J [auth B] SDF format, chain IA [auth A] SDF format, chain I [auth B] SDF format, chain HA [auth A] SDF format, chain H [auth B] SDF format, chain GB [auth E] SDF format, chain GA [auth A] SDF format, chain G [auth B] SDF format, chain FA [auth A] SDF format, chain F [auth B] SDF format, chain EA [auth A] SDF format, chain DA [auth A] SDF format, chain CA [auth A] SDF format, chain BA [auth A] SDF format, chain AA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain WA [auth D] MOL2 format, chain W [auth A] MOL2 format, chain VA [auth D] MOL2 format, chain V [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain MB [auth C] MOL2 format, chain M [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain JA [auth A] MOL2 format, chain J [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain I [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain H [auth B] MOL2 format, chain GB [auth E] MOL2 format, chain GA [auth A] MOL2 format, chain G [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain F [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain WA [auth D] mmCIF format, chain W [auth A] mmCIF format, chain VA [auth D] mmCIF format, chain V [auth A] mmCIF format, chain UA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain MB [auth C] mmCIF format, chain M [auth B] mmCIF format, chain LB [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain JA [auth A] mmCIF format, chain J [auth B] mmCIF format, chain IA [auth A] mmCIF format, chain I [auth B] mmCIF format, chain HA [auth A] mmCIF format, chain H [auth B] mmCIF format, chain GB [auth E] mmCIF format, chain GA [auth A] mmCIF format, chain G [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain F [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth A] AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], F [auth B], FA [auth A], G [auth B], GA [auth A], GB [auth E], H [auth B], HA [auth A], I [auth B], IA [auth A], J [auth B], JA [auth A], K [auth B], L [auth B], LB [auth C], M [auth B], MB [auth C], RA [auth D], SA [auth D], TA [auth D], UA [auth D], V [auth A], VA [auth D], W [auth A], WA [auth D], X [auth A], Y [auth A], Z [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain F [auth B] Focus chain FA [auth A] Focus chain G [auth B] Focus chain GA [auth A] Focus chain GB [auth E] Focus chain H [auth B] Focus chain HA [auth A] Focus chain I [auth B] Focus chain IA [auth A] Focus chain J [auth B] Focus chain JA [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain LB [auth C] Focus chain M [auth B] Focus chain MB [auth C] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain V [auth A] Focus chain VA [auth D] Focus chain W [auth A] Focus chain WA [auth D] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain F [auth B] Focus chain FA [auth A] Focus chain G [auth B] Focus chain GA [auth A] Focus chain GB [auth E] Focus chain H [auth B] Focus chain HA [auth A] Focus chain I [auth B] Focus chain IA [auth A] Focus chain J [auth B] Focus chain JA [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain LB [auth C] Focus chain M [auth B] Focus chain MB [auth C] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain V [auth A] Focus chain VA [auth D] Focus chain W [auth A] Focus chain WA [auth D] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain ZA [auth D] SDF format, chain QB [auth C] SDF format, chain Q [auth B] SDF format, chain PB [auth C] SDF format, chain P [auth B] SDF format, chain NA [auth A] SDF format, chain MA [auth A] SDF format, chain KB [auth E] SDF format, chain JB [auth E] SDF format, chain AB [auth D] MOL2 format, chain ZA [auth D] MOL2 format, chain QB [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain PB [auth C] MOL2 format, chain P [auth B] MOL2 format, chain NA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain KB [auth E] MOL2 format, chain JB [auth E] MOL2 format, chain AB [auth D] mmCIF format, chain ZA [auth D] mmCIF format, chain QB [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain PB [auth C] mmCIF format, chain P [auth B] mmCIF format, chain NA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain KB [auth E] mmCIF format, chain JB [auth E] mmCIF format, chain AB [auth D]	AB [auth D] JB [auth E] KB [auth E] MA [auth A] NA [auth A] AB [auth D], JB [auth E], KB [auth E], MA [auth A], NA [auth A], P [auth B], PB [auth C], Q [auth B], QB [auth C], ZA [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain JB [auth E] Focus chain KB [auth E] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain P [auth B] Focus chain PB [auth C] Focus chain Q [auth B] Focus chain QB [auth C] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain JB [auth E] Focus chain KB [auth E] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain P [auth B] Focus chain PB [auth C] Focus chain Q [auth B] Focus chain QB [auth C] Focus chain ZA [auth D]