9DZ7 | pdb_00009dz7

Structure of ALAS bound to glycine from S. cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb9DZ7/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-10-15 Released: 2025-10-22 
• Deposition Author(s): Tran, J.U., Brown, B.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), American Heart Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.207 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Structure of ALAS bound to glycine from S. cerevisiae

Tran, J.U., Brown, B.L.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 328.1 kDa 
• Atom Count: 22,739 
• Modeled Residue Count: 2,812 
• Deposited Residue Count: 2,946 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-aminolevulinate synthase, mitochondrial	A [auth F], B [auth A], C, D [auth E], E [auth D], F [auth B]	491	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: HEM1, CYD1, YDR232W, YD9934.16 EC: 2.3.1.37
UniProt
Find proteins for P09950 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P09950  Go to UniProtKB:  P09950

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLG (Subject of Investigation/LOI)	FA [auth D], G [auth F], H [auth A], HA [auth B], O [auth C], T [auth E]	N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] C10 H15 N2 O7 P FEVQWBMNLWUBTF-UHFFFAOYSA-N
PEG	AA [auth E], BA [auth E], CA [auth E], DA [auth E], EA [auth E], GA [auth D], I [auth A], IA [auth B], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], P [auth C], Q [auth C], R [auth C], S [auth C], U [auth E], V [auth E], W [auth E], X [auth E], Y [auth E], Z [auth E]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.207 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.672	α = 115.76
b = 112.518	β = 98.31
c = 117.388	γ = 91.49

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Tran, J.U., Brown, B.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	DP2GM146255
American Heart Association	United States	24PRE1190012

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release