4ORO | pdb_00004oro

Structure of Influenza B PB2 cap-binding domain complex with GDP

PDB DOI: https://doi.org/10.2210/pdb4ORO/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza B virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-02-11 Released: 2015-05-20
Deposition Author(s): Liu, Y., Zheng, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.270 (Depositor), 0.261 (DCC)
R-Value Work:
0.199 (Depositor), 0.197 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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Literature

Structure of Influenza B PB2 cap-binding domain complex with GDP

Liu, Y., Zheng, X.

To be published.

Macromolecule Content

Total Structure Weight: 80.22 kDa
Atom Count: 5,819
Modeled Residue Count: 676
Deposited Residue Count: 676
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase PB2	A, B, C, D	169	Influenza B virus	Mutation(s): 0
UniProt
Find proteins for A0A0M3KKU8 (Influenza B virus) Explore A0A0M3KKU8 Go to UniProtKB: A0A0M3KKU8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0M3KKU8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.270 (Depositor), 0.261 (DCC)
R-Value Work: 0.199 (Depositor), 0.197 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.42	α = 90
b = 42.771	β = 90.08
c = 118.414	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-05-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-05-20
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.