9PGY | pdb_00009pgy

Crystal structure of STEAP2 N-domain in complex with NADPH

• PDB DOI: https://doi.org/10.2210/pdb9PGY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-07-08 Released: 2025-10-29 
• Deposition Author(s): Shin, I., Liu, A.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.200 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of STEAP2 N-Domain with Its Bound NADPH Redox State Validated by Single-Crystal Spectroscopy

Shin, I., Liu, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 21.46 kDa 
• Atom Count: 1,700 
• Modeled Residue Count: 179 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metalloreductase STEAP2	A	182	Homo sapiens	Mutation(s): 3  Gene Names: STEAP2, PCANAP1, STAMP1, UNQ6507/PRO23203 EC: 1.16.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFT2 (Homo sapiens) Explore Q8NFT2  Go to UniProtKB:  Q8NFT2
PHAROS:  Q8NFT2 GTEx:  ENSG00000157214

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP (Subject of Investigation/LOI)	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.200 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.218	α = 90
b = 68.218	β = 90
c = 95.398	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
DENZO	data reduction
PHENIX	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Shin, I., Liu, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA247379

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release