6IE2 | pdb_00006ie2

Crystal structure of methyladenine demethylase

• PDB DOI: https://doi.org/10.2210/pdb6IE2/pdb

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


• Deposited: 2018-09-13 Released: 2019-09-18 
• Deposition Author(s): Tian, L.F., Tang, Q., Chen, Z.Z., Yan, X.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.254 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Structural basis of nucleic acid recognition and 6mA demethylation by human ALKBH1.

Tian, L.F., Liu, Y.P., Chen, L., Tang, Q., Wu, W., Sun, W., Chen, Z., Yan, X.X.

(2020) Cell Res 30: 272-275

• PubMed: 32051559 
• DOI: https://doi.org/10.1038/s41422-019-0233-9
• Primary Citation of Related Structures:  
  6IE2, 6IE3

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Organizational Affiliation: 
• State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China.
National Laboratory of Biomacromolecules, Chinese Academy of Sciences (CAS) Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China.
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China. [e-mail].
National Laboratory of Biomacromolecules, Chinese Academy of Sciences (CAS) Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Biological Assembly 7  

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

Biological assembly 7 assigned by authors.

Biological Assembly 8  

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

Biological assembly 8 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 352.71 kDa 
• Atom Count: 20,660 
• Modeled Residue Count: 2,578 
• Deposited Residue Count: 3,112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleic acid dioxygenase ALKBH1	A, B, C, D, E, F, G, H	389	Homo sapiens	Mutation(s): 0  Gene Names: ALKBH1, ABH, ABH1, ALKBH EC: 1.14.11.51 (PDB Primary Data), 1.14.11 (UniProt), 1.14.11.33 (UniProt), 4.2.99.18 (UniProt)
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
AKG	J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
MN	I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.254 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.017	α = 106.6
b = 99.17	β = 90.42
c = 126.793	γ = 93.14

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-18 
Deposition Author(s): Tian, L.F., Tang, Q., Chen, Z.Z., Yan, X.X.

Revision History  

• Version 1.0: 2019-09-18
  Type: Initial release
  
• Version 1.1: 2020-07-08
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description