6STT | pdb_00006stt

Adenovirus 29 Fiber Knob protein in complex with Sialic acid

PDB DOI: https://doi.org/10.2210/pdb6STT/pdb

Classification: VIRAL PROTEIN
Organism(s): Human adenovirus 29
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-09-11 Released: 2021-03-31
Deposition Author(s): Baker, A.T., Mundy, R.M., Rizkallah, P.J., Parker, A.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.188 (Depositor), 0.191 (DCC)
R-Value Work:
0.140 (Depositor), 0.150 (DCC)
R-Value Observed:
0.142 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Broad sialic acid usage amongst species D human adenovirus

Mundy, R.M., Baker, A.T., Bates, E.A., Cunliffe, T.G., Teijeira-Crespo, A., Moses, E., Rizkallah, P.J., Parker, A.L.

(2023) Npj Viruses 1: 1

DOI: https://doi.org/10.1038/s44298-023-00001-5

Macromolecule Content

Total Structure Weight: 42.61 kDa
Atom Count: 3,290
Modeled Residue Count: 356
Deposited Residue Count: 370
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fiber	A, B	185	Human adenovirus 29	Mutation(s): 0 Gene Names: L5
UniProt
Find proteins for E1CIQ3 (Human adenovirus 29) Explore E1CIQ3 Go to UniProtKB: E1CIQ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E1CIQ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA (Subject of Investigation/LOI) Query on SIA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.188 (Depositor), 0.191 (DCC)
R-Value Work: 0.140 (Depositor), 0.150 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: P 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.236	α = 90
b = 104.236	β = 90
c = 104.236	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-03-31

Deposition Author(s):

Rizkallah, P.J.

Revision History (Full details and data files)

Version 1.0: 2021-03-31
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references
Version 1.2: 2023-10-11
Changes: Database references

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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.