4ORO

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
R-Value Work: 0.199
R-Value Observed: 0.203

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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
Modelled Residue Count: 676
Deposited Residue Count: 676
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	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
R-Value Work: 0.199
R-Value Observed: 0.203
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):

Liu, Y.

Zheng, X.

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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4ORO

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)