9I2O | pdb_00009i2o

PB2 cap-binding domain of human pathogenic influenza A virus H5N1 in complex with m7GTP

PDB DOI: https://doi.org/10.2210/pdb9I2O/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Influenza A virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-01-21 Released: 2025-01-29
Deposition Author(s): Falke, S., Lewe, P., Witt, S., Wrenger, C., Meents, A.
Funding Organization(s): Helmholtz Association, German Federal Ministry for Education and Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.206 (Depositor), 0.206 (DCC)
R-Value Work:
0.182 (Depositor), 0.182 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9I2O

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

PB2 cap-binding domain of human pathogenic influenza A virus H5N1 in complex with m7GTP

Falke, S., Lewe, P., Witt, S., Wrenger, C., Meents, A.

To be published.

Macromolecule Content

Total Structure Weight: 21.91 kDa
Atom Count: 1,432
Modeled Residue Count: 163
Deposited Residue Count: 188
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase basic protein 2	A	188	Influenza A virus	Mutation(s): 0 Gene Names: PB2
UniProt
Find proteins for Q6DNL8 (Influenza A virus (strain A/Chicken/Hong Kong/YU22/2002 H5N1 genotype Z)) Explore Q6DNL8 Go to UniProtKB: Q6DNL8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6DNL8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGT (Subject of Investigation/LOI) Query on MGT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE C₁₁ H₂₀ N₅ O₁₄ P₃ BUJQMJUTTBGELS-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.206 (Depositor), 0.206 (DCC)
R-Value Work: 0.182 (Depositor), 0.182 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.75	α = 90
b = 81.75	β = 90
c = 55.009	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHENIX	phasing
XSCALE	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--
German Federal Ministry for Education and Research	Germany	--

Revision History (Full details and data files)

Version 1.0: 2025-01-29
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.