6MEA | pdb_00006mea

Crystal structure of a Tylonycteris bat coronavirus HKU4 macrodomain in complex with adenosine diphosphate ribose (ADP-ribose)

PDB DOI: https://doi.org/10.2210/pdb6MEA/pdb

Classification: HYDROLASE
Organism(s): Tylonycteris bat coronavirus HKU4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-09-06 Released: 2019-09-11
Deposition Author(s): Hammond, R.G., Schormann, N., McPherson, R.L., Leung, A.K.L., Deivanayagam, C.C.S., Johnson, M.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.162 (Depositor), 0.162 (DCC)
R-Value Work:
0.142 (Depositor), 0.142 (DCC)
R-Value Observed:
0.143 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

ADP-Ribose and Analogues bound to the DeMARylating Macrodomain from the Bat Coronavirus HKU4

Hammond, R.G., Schormann, N., McPherson, R.L., Leung, A.K.L., Deivanayagam, C., Johnson, M.A.

(2021) Proc Natl Acad Sci U S A

DOI: https://doi.org/10.1073/pnas.2004500118

Macromolecule Content

Total Structure Weight: 38.31 kDa
Atom Count: 2,884
Modeled Residue Count: 323
Deposited Residue Count: 348
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1ab	A, B	174	Tylonycteris bat coronavirus HKU4	Mutation(s): 0 Gene Names: rep, 1a-1b
UniProt
Find proteins for P0C6W3 (Bat coronavirus HKU4) Explore P0C6W3 Go to UniProtKB: P0C6W3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C6W3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
APR Query on APR Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	ADENOSINE-5-DIPHOSPHORIBOSE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-KEOHHSTQSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.162 (Depositor), 0.162 (DCC)
R-Value Work: 0.142 (Depositor), 0.142 (DCC)
R-Value Observed: 0.143 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.614	α = 73.16
b = 41.642	β = 88.29
c = 59.783	γ = 88.25

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-09-11

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM119456

Revision History (Full details and data files)

Version 1.0: 2019-09-11
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2021-01-13
Changes: Database references
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Refinement description