9TAB | pdb_00009tab

Crystal Structure of Human Adenovirus 52 Short Fiber Knob Mutant N243R in Complex with alpha-(2,8)-Pentasialic Acid (DP5)

PDB DOI: https://doi.org/10.2210/pdb9TAB/pdb

Classification: VIRAL PROTEIN
Organism(s): human adenovirus 52
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-11-18 Released: 2026-08-26
Deposition Author(s): Vonmetz, K., Stehle, T.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.201 (Depositor), 0.202 (DCC)
R-Value Work:
0.163 (Depositor), 0.164 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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Literature

Crystal Structures of Human Adenovirus 52 Short Fiber Knob Mutants in Complex with alpha-(2,8)-Pentasialic Acid (DP5)

Vonmetz, K., Stehle, T.

To be published.

Macromolecule Content

Total Structure Weight: 67.82 kDa
Atom Count: 4,399
Modeled Residue Count: 504
Deposited Residue Count: 627
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fiber-1	A, B, C	209	human adenovirus 52	Mutation(s): 1
UniProt
Find proteins for A0MK70 (human adenovirus 52) Explore A0MK70 Go to UniProtKB: A0MK70
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0MK70
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 E [auth C] MOL2 format, chain E [auth C] mmCIF format, chain E [auth C]	E [auth C]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.201 (Depositor), 0.202 (DCC)
R-Value Work: 0.163 (Depositor), 0.164 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.446	α = 90
b = 82.268	β = 90
c = 93.421	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	FOR2953

Revision History (Full details and data files)

Version 1.0: 2026-08-26
Type: Initial release

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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.