9NCZ | pdb_00009ncz

Crystal structure of human AlkBH3 in complex with manganese and 2-oxoglutarate

• PDB DOI: https://doi.org/10.2210/pdb9NCZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-02-17 Released: 2025-03-12 
• Deposition Author(s): Suma, K., Mugridge, J.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.242 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 

Starting Model: experimental

Literature

Crystal structure of human AlkBH3 in complex with manganese and 2-oxoglutarate

Suma, K., Mugridge, J.S.

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: 29.31 kDa 
• Atom Count: 1,894 
• Modeled Residue Count: 214 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3	A	250	Homo sapiens	Mutation(s): 0  Gene Names: ALKBH3, ABH3, DEPC1 EC: 1.14.11.33 (PDB Primary Data), 1.14.11.54 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96Q83 (Homo sapiens) Explore Q96Q83  Go to UniProtKB:  Q96Q83
PHAROS:  Q96Q83 GTEx:  ENSG00000166199

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG	C [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.242 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.496	α = 90
b = 66.031	β = 101.199
c = 51.857	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Suma, K., Mugridge, J.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM143000

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release