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

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of ALAS bound to glycine from S. cerevisiae

Tran, J.U., Brown, B.L.

To be published.

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

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(by identity cutoff) | 3D Structure

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] 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09950
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLG (Subject of Investigation/LOI) Query on PLG Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain G [auth F] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain O [auth C] SDF format, chain T [auth E] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth F] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth E] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth F] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain O [auth C] mmCIF format, chain T [auth E]	FA [auth D] G [auth F] H [auth A] HA [auth B] O [auth C] 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		Interactions Focus chain FA [auth D] Focus chain G [auth F] Focus chain H [auth A] Focus chain HA [auth B] Focus chain O [auth C] Focus chain T [auth E] Interactions & Density Focus chain FA [auth D] Focus chain G [auth F] Focus chain H [auth A] Focus chain HA [auth B] Focus chain O [auth C] Focus chain T [auth E]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain GA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain X [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth E] SDF format, chain W [auth E] SDF format, chain IA [auth B] SDF format, chain EA [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain GA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain W [auth E] MOL2 format, chain IA [auth B] MOL2 format, chain EA [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain GA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain U [auth E] mmCIF format, chain V [auth E] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain W [auth E] mmCIF format, chain IA [auth B] mmCIF format, chain EA [auth E]	AA [auth E] BA [auth E] CA [auth E] DA [auth E] EA [auth E] 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		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain GA [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain GA [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Tran, J.U.

Brown, B.L.

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