9EMV

SARS-CoV-2 nsp10-16 methyltransferase in complex with Sangivamycin and m7GpppA (Cap0-analog)/m7GpppAm (Cap1-analog)

PDB DOI: https://doi.org/10.2210/pdb9EMV/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-03-11 Released: 2024-03-20
Deposition Author(s): Kremling, V., Sprenger, J., Oberthuer, D., Scheer, T.E.S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.256
R-Value Work: 0.203
R-Value Observed: 0.205

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug discovery

Kremling, V., Falke, S., Fernandez-Garcia, Y., Ehrt, C., Kiene, A., Klopprogge, B., Scheer, E., Barthels, F., Middendorf, P., Kuhn, S., Gunther, S., Rarey, M., Chapman, H.N., Oberthur, D., Sprenger, J.

(2024) Elife

DOI: https://doi.org/10.7554/elife.98310.1

Macromolecule Content

Total Structure Weight: 52.12 kDa
Atom Count: 3,585
Modelled Residue Count: 415
Deposited Residue Count: 444
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2'-O-methyltransferase nsp16	A	304	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 2.1.1.57
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 10	B	140	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
V9G (Subject of Investigation/LOI) Query on V9G Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-(2'-O-METHYL)-ADENOSINE C₂₂ H₃₂ N₁₀ O₁₇ P₃ WZAAWBDISKLAIE-NAGRZYTCSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
GTA (Subject of Investigation/LOI) Query on GTA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE C₂₁ H₃₀ N₁₀ O₁₇ P₃ QQOHNVHGNZYSBP-XPWFQUROSA-O		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SGV (Subject of Investigation/LOI) Query on SGV Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SANGIVAMYCIN C₁₂ H₁₅ N₅ O₅ OBZJZDHRXBKKTJ-JTFADIMSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B]	N [auth B], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain N [auth B] Focus chain O [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain Q [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth B]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], P [auth B], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.256
R-Value Work: 0.203
R-Value Observed: 0.205
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.51	α = 90
b = 169.51	β = 90
c = 52.25	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHENIX	refinement
Coot	model building
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	Germany	DESY Strategy Fund MUXCOSDYN

Revision History (Full details and data files)

Version 1.0: 2024-03-20
Type: Initial release
Version 2.0: 2024-11-13
Changes: Atomic model, Data collection, Database references, Structure summary