7XXK

Crystal structure of SARS-CoV-2 N-CTD in complex with GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of SARS-CoV-2 N-CTD in complex with GMP

Zhou, R.J.Ni, X.C.Lei, J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoprotein
A, B, C, D, E
A, B, C, D, E, F
120Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC9 
Go to UniProtKB:  P0DTC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5GP (Subject of Investigation/LOI)
Query on 5GP

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
S [auth C]
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
GMP (Subject of Investigation/LOI)
Query on GMP

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FA [auth F]GUANOSINE
C10 H13 N5 O5
NYHBQMYGNKIUIF-UUOKFMHZSA-N
GUN (Subject of Investigation/LOI)
Query on GUN

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R [auth C]GUANINE
C5 H5 N5 O
UYTPUPDQBNUYGX-UHFFFAOYSA-N
SCN
Query on SCN

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G [auth A]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
K
Query on K

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AA [auth D]
BA [auth D]
GA [auth F]
J [auth A]
K [auth A]
AA [auth D],
BA [auth D],
GA [auth F],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth B],
T [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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CA [auth D]
DA [auth E]
EA [auth E]
HA [auth F]
IA [auth F]
CA [auth D],
DA [auth E],
EA [auth E],
HA [auth F],
IA [auth F],
O [auth B],
P [auth B],
Q [auth B],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
JA [auth F],
Z [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.783α = 90
b = 116.992β = 90
c = 127.039γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2021YFF0702004

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description