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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.254 (Depositor), 0.226 (DCC)
R-Value Work:
0.216 (Depositor), 0.223 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41422-019-0233-9
Primary Citation Related Structures:
6IE2, 6IE3

Organizational Affiliation

State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China.

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

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleic acid dioxygenase ALKBH1	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13686
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AKG Query on AKG Download:Ideal Coordinates CCD File SDF format, chain X [auth H] SDF format, chain V [auth G] SDF format, chain T [auth F] SDF format, chain R [auth E] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] MOL2 format, chain X [auth H] MOL2 format, chain V [auth G] MOL2 format, chain T [auth F] MOL2 format, chain R [auth E] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] mmCIF format, chain X [auth H] mmCIF format, chain V [auth G] mmCIF format, chain T [auth F] mmCIF format, chain R [auth E] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A]	J [auth A] L [auth B] N [auth C] P [auth D] R [auth E] 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		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain W [auth H] SDF format, chain U [auth G] SDF format, chain S [auth F] SDF format, chain Q [auth E] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain W [auth H] MOL2 format, chain U [auth G] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain W [auth H] mmCIF format, chain U [auth G] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] 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		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.254 (Depositor), 0.226 (DCC)
R-Value Work: 0.216 (Depositor), 0.223 (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

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Entry History

Deposition Data

Released Date: 2019-09-18

Deposition Author(s):

Revision History (Full details and data files)

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

6IE2 | pdb_00006ie2

Crystal structure of methyladenine demethylase

Literature

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

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Biological Assembly 6

Biological Assembly 7

Biological Assembly 8

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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