8K62

Crystal structure of ALKBH1 and 13h complex.

• PDB DOI: https://doi.org/10.2210/pdb8K62/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-24 Released: 2024-07-31 
• Deposition Author(s): Liang, X., Yinping, G., Feng, L., Jiang, Z., Ke, X., Shengyong, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.278 
• R-Value Work: 0.204 
• R-Value Observed: 0.211 

Starting Model: experimental

Literature

Crystal structure of ALKBH1 and 13h complex

Liang, X., Yinping, G., Ke, X., Shengyong, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 44.32 kDa 
• Atom Count: 2,682 
• Modelled Residue Count: 326 
• Deposited Residue Count: 389 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleic acid dioxygenase ALKBH1	A	389	Homo sapiens	Mutation(s): 0  Gene Names: ALKBH1, ABH, ABH1, ALKBH EC: 1.14.11 (PDB Primary Data), 1.14.11.51 (PDB Primary Data), 4.2.99.18 (PDB Primary Data), 1.14.11.33 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13686 (Homo sapiens) Explore Q13686  Go to UniProtKB:  Q13686
GTEx:  ENSG00000100601

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IAU	C [auth A]	1-[5-[[3-(trifluoromethyloxy)phenyl]methoxy]pyrimidin-2-yl]pyrazole-4-carboxylic acid C16 H11 F3 N4 O4 LCLDWDBSMQPBKO-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.278 
• R-Value Work: 0.204 
• R-Value Observed: 0.211 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.502	α = 90
b = 56.502	β = 90
c = 192.135	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Liang, X., Yinping, G., Feng, L., Jiang, Z., Ke, X., Shengyong, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81930125

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release