3QND

crystal structure of Ad37 fiber knob in complex with trivalent sialic acid inhibitor

PDB DOI: https://doi.org/10.2210/pdb3QND/pdb

Classification: CELL ADHESION/INHIBITOR
Organism(s): Human adenovirus D37
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-02-08 Released: 2011-06-15
Deposition Author(s): Stehle, T., Bauer, J., Elofsson, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.263
R-Value Work: 0.221
R-Value Observed: 0.223

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

A potent trivalent sialic Acid inhibitor of adenovirus type 37 infection of human corneal cells.

Spjut, S., Qian, W., Bauer, J., Storm, R., Frangsmyr, L., Stehle, T., Arnberg, N., Elofsson, M.

(2011) Angew Chem Int Ed Engl 50: 6519-6521

PubMed: 21648036 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/anie.201101559
Primary Citation of Related Structures:
3QND

Organizational Affiliation

Department of Chemistry, Umeå Centre for Microbial Research (UCMR) and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden.

Macromolecule Content

Total Structure Weight: 132.61 kDa
Atom Count: 9,095
Modelled Residue Count: 1,104
Deposited Residue Count: 1,164
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fiber protein	A B C D [auth E] E [auth F] A, B, C, D [auth E], E [auth F], F [auth G]	194	Human adenovirus D37	Mutation(s): 0 Gene Names: L5
UniProt
Find proteins for Q64823 (Human adenovirus D37) Explore Q64823 Go to UniProtKB: Q64823
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q64823
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SIA Query on SIA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain O [auth E] SDF format, chain Q [auth F] SDF format, chain S [auth G] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain S [auth G]	H [auth A] J [auth B] L [auth C] O [auth E] Q [auth F] H [auth A], J [auth B], L [auth C], O [auth E], Q [auth F], S [auth G]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth E] Focus chain Q [auth F] Focus chain S [auth G] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth E] Focus chain Q [auth F] Focus chain S [auth G]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth E] SDF format, chain N [auth E] SDF format, chain P [auth F] SDF format, chain R [auth G] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth E] MOL2 format, chain N [auth E] MOL2 format, chain P [auth F] MOL2 format, chain R [auth G]	G [auth A] I [auth B] K [auth C] M [auth E] N [auth E] G [auth A], I [auth B], K [auth C], M [auth E], N [auth E], P [auth F], R [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth E] Focus chain N [auth E] Focus chain P [auth F] Focus chain R [auth G] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth E] Focus chain N [auth E] Focus chain P [auth F] Focus chain R [auth G]

Binding Affinity Annotations
ID	Source	Binding Affinity
SIA	PDBBind: 3QND	Kd: 1.40e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.263
R-Value Work: 0.221
R-Value Observed: 0.223
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.19	α = 90
b = 108.645	β = 90
c = 112.511	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-06-15

Deposition Author(s):

Stehle, T.

Bauer, J.

Elofsson, M.

Revision History (Full details and data files)

Version 1.0: 2011-06-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-08-10
Changes: Database references
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

3QND

crystal structure of Ad37 fiber knob in complex with trivalent sialic acid inhibitor

A potent trivalent sialic Acid inhibitor of adenovirus type 37 infection of human corneal cells.

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)