7B6A

BK Polyomavirus VP1 pentamer core (residues 30-299)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Discovery of novel druggable pockets on polyomavirus VP1 through crystallographic fragment-based screening to develop capsid assembly inhibitors

Osipov, E.M.Munawar, A.H.Beelen, S.Fearon, D.Douangamath, A.Wild, C.Weeks, S.D.Van Aerschot, A.von Delft, F.Strelkov, S.V.

(2022) RSC Chem Biol 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major capsid protein VP1A [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD],
E [auth EEE]
270Human polyomavirus 1Mutation(s): 0 
UniProt
Find proteins for P03088 (BK polyomavirus)
Explore P03088 
Go to UniProtKB:  P03088
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03088
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
BA [auth CCC],
CA [auth CCC],
DA [auth CCC],
EA [auth CCC],
FA [auth CCC],
BA [auth CCC],
CA [auth CCC],
DA [auth CCC],
EA [auth CCC],
FA [auth CCC],
M [auth AAA],
MA [auth DDD],
N [auth AAA],
NA [auth DDD],
O [auth AAA],
OA [auth DDD],
TA [auth EEE],
U [auth BBB],
UA [auth EEE],
V [auth BBB],
VA [auth EEE]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
AA [auth CCC],
JA [auth DDD],
K [auth AAA],
KA [auth DDD],
L [auth AAA],
AA [auth CCC],
JA [auth DDD],
K [auth AAA],
KA [auth DDD],
L [auth AAA],
LA [auth DDD],
RA [auth EEE],
S [auth BBB],
SA [auth EEE],
T [auth BBB],
Y [auth CCC],
Z [auth CCC]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth AAA],
G [auth AAA],
GA [auth DDD],
H [auth AAA],
HA [auth DDD],
F [auth AAA],
G [auth AAA],
GA [auth DDD],
H [auth AAA],
HA [auth DDD],
I [auth AAA],
IA [auth DDD],
J [auth AAA],
Q [auth BBB],
QA [auth EEE],
R [auth BBB],
W [auth CCC],
X [auth CCC]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
P [auth AAA],
PA [auth DDD]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.622α = 90
b = 149.719β = 90
c = 65.488γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)BelgiumG0A5718N

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release