6Y73

The crystal structure of human MACROD2 in space group P43

PDB DOI: https://doi.org/10.2210/pdb6Y73/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-02-28 Released: 2020-09-30
Deposition Author(s): Wazir, S., Maksimainen, M.M., Lehtio, L.
Funding Organization(s): Academy of Finland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.203
R-Value Work: 0.182
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

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

Literature

Multiple crystal forms of human MacroD2.

Wazir, S., Maksimainen, M.M., Lehtio, L.

(2020) Acta Crystallogr F Struct Biol Commun 76: 477-482

PubMed: 33006575 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X20011309
Primary Citation of Related Structures:
6Y4Y, 6Y4Z, 6Y73

PubMed Abstract:
MacroD2 is one of the three human macrodomain proteins characterized by their protein-linked mono-ADP-ribosyl-hydrolyzing activity. MacroD2 is a single-domain protein that contains a deep ADP-ribose-binding groove. In this study, new crystallization conditions for MacroD2 were found and three crystal structures of human MacroD2 in the apo state were solved in space groups P4 ₁2 ₁2, P4 ₃2 ₁2 and P4 ₃, and refined at 1.75, 1.90 and 1.70 Å resolution, respectively. Structural comparison of the apo crystal structures with the previously reported crystal structure of MacroD2 in complex with ADP-ribose revealed conformational changes in the side chains of Val101, Ile189 and Phe224 induced by the binding of ADP-ribose in the active site. These conformational variations may potentially facilitate design efforts of a MacroD2 inhibitor.

Organizational Affiliation

Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5400, Oulu 90014, Finland.

Macromolecule Content

Total Structure Weight: 328.62 kDa
Atom Count: 15,593
Modelled Residue Count: 1,729
Deposited Residue Count: 2,928
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribose glycohydrolase MACROD2	A, B, C, D, E A, B, C, D, E, F, G, H	366	Homo sapiens	Mutation(s): 0 Gene Names: MACROD2, C20orf133 EC: 3.5.1 (PDB Primary Data), 3.2.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for A1Z1Q3 (Homo sapiens) Explore A1Z1Q3 Go to UniProtKB: A1Z1Q3
PHAROS: A1Z1Q3 GTEx: ENSG00000172264
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1Z1Q3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain Q [auth F] SDF format, chain S [auth G] SDF format, chain T [auth H] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth F] MOL2 format, chain S [auth G] MOL2 format, chain T [auth H]	K [auth B], L [auth C], Q [auth F], S [auth G], T [auth H]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain K [auth B] Focus chain L [auth C] Focus chain Q [auth F] Focus chain S [auth G] Focus chain T [auth H] Interactions & Density Focus chain K [auth B] Focus chain L [auth C] Focus chain Q [auth F] Focus chain S [auth G] Focus chain T [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain O [auth C] SDF format, chain P [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D]	I [auth A], J [auth B], M [auth C], O [auth C], P [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth C] Focus chain P [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth C] Focus chain P [auth D]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain R [auth F] MOL2 format, chain N [auth C] MOL2 format, chain R [auth F]	N [auth C], R [auth F]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Focus chain R [auth F] Interactions & Density Focus chain N [auth C] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.203
R-Value Work: 0.182
R-Value Observed: 0.183
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.78	α = 90
b = 96.78	β = 90
c = 261.09	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-09-30

Deposition Author(s):

Wazir, S.

Maksimainen, M.M.

Lehtio, L.

Funding Organization	Location	Grant Number
Academy of Finland	Finland	287063
Academy of Finland	Finland	294085

Revision History (Full details and data files)

Version 1.0: 2020-09-30
Type: Initial release
Version 1.1: 2020-10-14
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description