6QPN | pdb_00006qpn

Adenovirus species D serotype 49 Fiber-Knob

PDB DOI: https://doi.org/10.2210/pdb6QPN/pdb

Classification: VIRAL PROTEIN
Organism(s): Human adenovirus 49
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-02-14 Released: 2020-08-26
Deposition Author(s): Baker, A.T., Rizkallah, P.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free:
0.259 (Depositor), 0.254 (DCC)
R-Value Work:
0.211 (Depositor), 0.212 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6QPN

This is version 2.2 of the entry. See complete history.

Literature

The Fiber Knob Protein of Human Adenovirus Type 49 Mediates Highly Efficient and Promiscuous Infection of Cancer Cell Lines Using a Novel Cell Entry Mechanism

Baker, A.T., Rizkallah, P.J.

(2021) Journal Of Virology 95

DOI: https://doi.org/10.1128/JVI.01849-20

Macromolecule Content

Total Structure Weight: 150.71 kDa
Atom Count: 9,083
Modeled Residue Count: 1,165
Deposited Residue Count: 1,356
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fiber	A, B, C, D, E A, B, C, D, E, F	226	Human adenovirus 49	Mutation(s): 0
UniProt
Find proteins for Q09TX9 (Human adenovirus 49) Explore Q09TX9 Go to UniProtKB: Q09TX9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q09TX9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain I [auth D] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain I [auth D] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B], I [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free: 0.259 (Depositor), 0.254 (DCC)
R-Value Work: 0.211 (Depositor), 0.212 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.83	α = 90
b = 56.28	β = 112.95
c = 115.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-08-26

Deposition Author(s):

Rizkallah, P.J.

Revision History (Full details and data files)

Version 1.0: 2020-08-26
Type: Initial release
Version 2.0: 2021-08-25
Type: Coordinate replacement
Reason: Atomic clashes
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.1: 2024-01-24
Changes: Data collection, Refinement description
Version 2.2: 2024-10-09
Changes: Structure summary

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.