Macromolecule Content

Total Structure Weight: 152.14 kDa
Atom Count: 11960
Modelled Residue Count: 1318
Deposited Residue Count: 1350
Unique protein chains: 1

7B6A

BK Polyomavirus VP1 pentamer core (residues 30-299)

PDB DOI: 10.2210/pdb7B6A/pdb

Classification: VIRAL PROTEIN
Organism(s): Human polyomavirus 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-12-07 Released: 2022-06-22
Deposition Author(s): Osipov, E.M., Munawar, A., Beelen, S., Strelkov, S.V.
Funding Organization(s): Research Foundation - Flanders (FWO)

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

DOI: 10.1039/D2CB00052K

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein VP1	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth EEE]	270	Human polyomavirus 1	Mutation(s): 0
UniProt
Find proteins for P03088 (BK polyomavirus) Explore P03088 Go to UniProtKB: P03088
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03088
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain CA [auth CCC] SDF format, chain DA [auth CCC] SDF format, chain EA [auth CCC] SDF format, chain FA [auth CCC] SDF format, chain M [auth AAA] SDF format, chain MA [auth DDD] SDF format, chain N [auth AAA] SDF format, chain O [auth AAA] SDF format, chain OA [auth DDD] SDF format, chain TA [auth EEE] SDF format, chain U [auth BBB] SDF format, chain UA [auth EEE] SDF format, chain V [auth BBB] SDF format, chain VA [auth EEE] SDF format, chain BA [auth CCC] SDF format, chain NA [auth DDD] MOL2 format, chain CA [auth CCC] MOL2 format, chain DA [auth CCC] MOL2 format, chain EA [auth CCC] MOL2 format, chain FA [auth CCC] MOL2 format, chain M [auth AAA] MOL2 format, chain MA [auth DDD] MOL2 format, chain N [auth AAA] MOL2 format, chain O [auth AAA] MOL2 format, chain OA [auth DDD] MOL2 format, chain TA [auth EEE] MOL2 format, chain U [auth BBB] MOL2 format, chain UA [auth EEE] MOL2 format, chain V [auth BBB] MOL2 format, chain VA [auth EEE] MOL2 format, chain BA [auth CCC] MOL2 format, chain NA [auth DDD]	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 SDF format, chain AA [auth CCC] SDF format, chain JA [auth DDD] SDF format, chain K [auth AAA] SDF format, chain KA [auth DDD] SDF format, chain L [auth AAA] SDF format, chain RA [auth EEE] SDF format, chain S [auth BBB] SDF format, chain SA [auth EEE] SDF format, chain T [auth BBB] SDF format, chain Y [auth CCC] SDF format, chain LA [auth DDD] SDF format, chain Z [auth CCC] MOL2 format, chain AA [auth CCC] MOL2 format, chain JA [auth DDD] MOL2 format, chain K [auth AAA] MOL2 format, chain KA [auth DDD] MOL2 format, chain L [auth AAA] MOL2 format, chain RA [auth EEE] MOL2 format, chain S [auth BBB] MOL2 format, chain SA [auth EEE] MOL2 format, chain T [auth BBB] MOL2 format, chain Y [auth CCC] MOL2 format, chain LA [auth DDD] MOL2 format, chain Z [auth CCC]	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 SDF format, chain G [auth AAA] SDF format, chain GA [auth DDD] SDF format, chain H [auth AAA] SDF format, chain HA [auth DDD] SDF format, chain I [auth AAA] SDF format, chain IA [auth DDD] SDF format, chain J [auth AAA] SDF format, chain Q [auth BBB] SDF format, chain QA [auth EEE] SDF format, chain R [auth BBB] SDF format, chain W [auth CCC] SDF format, chain X [auth CCC] SDF format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain GA [auth DDD] MOL2 format, chain H [auth AAA] MOL2 format, chain HA [auth DDD] MOL2 format, chain I [auth AAA] MOL2 format, chain IA [auth DDD] MOL2 format, chain J [auth AAA] MOL2 format, chain Q [auth BBB] MOL2 format, chain QA [auth EEE] MOL2 format, chain R [auth BBB] MOL2 format, chain W [auth CCC] MOL2 format, chain X [auth CCC] MOL2 format, chain F [auth AAA]	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 SDF format, chain P [auth AAA] SDF format, chain PA [auth DDD] MOL2 format, chain P [auth AAA] MOL2 format, chain PA [auth DDD]	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 = 138.622	α = 90
b = 149.719	β = 90
c = 65.488	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2020-12-07
Released Date: 2022-06-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G0A5718N

Revision History (Full details and data files)

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

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.