9DZO | pdb_00009dzo

Structure of ALAS bound to succinyl-CoA from S. cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb9DZO/pdb

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


• Deposited: 2024-10-16 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: 2.69 Å
• R-Value Free: 
  0.227 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.186 (DCC) 

Starting Model: experimental

Literature

Structure of ALAS bound to succinyl-CoA 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: 329.65 kDa 
• Atom Count: 23,215 
• Modeled Residue Count: 2,865 
• Deposited Residue Count: 2,946 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-aminolevulinate synthase, mitochondrial	A [auth C], B [auth D], C [auth A], D [auth E], E [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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5-aminolevulinate synthase, mitochondrial	F	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SCA (Subject of Investigation/LOI)	H [auth C], L [auth A], N [auth E], P [auth B], Q [auth F]	SUCCINYL-COENZYME A C25 H40 N7 O19 P3 S VNOYUJKHFWYWIR-ITIYDSSPSA-N
PLP (Subject of Investigation/LOI)	G [auth C], I [auth D], K [auth A], M [auth E], O [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
MG	J [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	F	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free:  0.227 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.186 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.595	α = 116.403
b = 114.241	β = 97.507
c = 119.307	γ = 91.839

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	DP2 GM146255
American Heart Association	United States	24PRE1190012

Revision History  

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