9FD0 | pdb_00009fd0

Structure of the Saccharomyces cerevisiae Pmt4-MIR domain with bound ligands

• PDB DOI: https://doi.org/10.2210/pdb9FD0/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-16 Released: 2025-11-26 
• Deposition Author(s): McDowell, M., Hackmann, Y., Wild, K., Sinning, I.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Structure of Chaetomium thermophilum Pmt4 with bound ligands

McDowell, M., Sinning, I.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.14 kDa 
• Atom Count: 2,042 
• Modeled Residue Count: 218 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dolichyl-phosphate-mannose--protein mannosyltransferase 4	A	222	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: PMT4, YJR143C, J2176 EC: 2.4.1.109
UniProt
Find proteins for P46971 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P46971  Go to UniProtKB:  P46971

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	B [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.593	α = 90
b = 56.767	β = 90
c = 78.216	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): McDowell, M., Hackmann, Y., Wild, K., Sinning, I.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release