6G47

Crystal Structure of Human Adenovirus 52 Short Fiber Knob in Complex with alpha-(2,8)-Trisialic Acid (DP3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.497 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Polysialic acid is a cellular receptor for human adenovirus 52.

Lenman, A.Liaci, A.M.Liu, Y.Frangsmyr, L.Frank, M.Blaum, B.S.Chai, W.Podgorski, I.I.Harrach, B.Benko, M.Feizi, T.Stehle, T.Arnberg, N.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E4264-E4273


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fiber-1
A, B, C
209Human adenovirus 52Mutation(s): 0 
Find proteins for A0MK70 (Human adenovirus 52)
Go to UniProtKB:  A0MK70
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download SDF File 
Download CCD File 
B
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, C
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
C
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
SIA
Query on SIA

Download SDF File 
Download CCD File 
A, C
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.497 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.880α = 90.00
b = 81.710β = 90.00
c = 93.530γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB 685

Revision History 

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-09
    Type: Data collection, Database references