5QR2 | pdb_00005qr2

PanDDA analysis group deposition -- Crystal Structure of human ALAS2A in complex with Z1348371854

• PDB DOI: https://doi.org/10.2210/pdb5QR2/pdb
• Deposition Group: G_1002078 (changed state) | Explore  G_1002078  

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-05-22 Released: 2019-08-07 
• Deposition Author(s): Bezerra, G.A., Foster, W., Bailey, H., Shrestha, L., Krojer, T., Talon, R., Brandao-Neto, J., Douangamath, A., Nicola, B.B., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Brennan, P.E., Yue, W.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.232 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

PanDDA analysis group deposition

Bezerra, G.A., Foster, W., Bailey, H., Shrestha, L., Krojer, T., Talon, R., Brandao-Neto, J., Douangamath, A., Nicola, B.B., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Brennan, P.E., Yue, W.W.

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)

Macromolecule Content 

• Total Structure Weight: 105.2 kDa 
• Atom Count: 6,919 
• Modeled Residue Count: 857 
• Deposited Residue Count: 938 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-aminolevulinate synthase, erythroid-specific, mitochondrial	A [auth B], B [auth A]	469	Homo sapiens	Mutation(s): 0  Gene Names: ALAS2, ALASE, ASB EC: 2.3.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for P22557 (Homo sapiens) Explore P22557  Go to UniProtKB:  P22557
PHAROS:  P22557 GTEx:  ENSG00000158578

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth B], D [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
NTG (Subject of Investigation/LOI)	E [auth A]	5-(1,4-oxazepan-4-yl)pyridine-2-carbonitrile C11 H13 N3 O QPJKHSFVBDONPD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.232 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.522	α = 90
b = 108.137	β = 109.11
c = 75.521	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-07 
Deposition Author(s): Bezerra, G.A., Foster, W., Bailey, H., Shrestha, L., Krojer, T., Talon, R., Brandao-Neto, J., Douangamath, A., Nicola, B.B., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Brennan, P.E., Yue, W.W.

Revision History  

• Version 1.0: 2019-08-07
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2026-02-18
  Changes: Refinement description, Structure summary