4POS
Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactosamine
- PDB DOI: https://doi.org/10.2210/pdb4POS/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Human polyomavirus 9
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No 
- Deposited: 2014-02-26 Released: 2014-04-09 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.213 
- R-Value Work: 0.179 
- R-Value Observed: 0.180 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
VP1 | 278 | Human polyomavirus 9 | Mutation(s): 0  Gene Names: gp3, vp1 | ||
UniProt | |||||
Find proteins for E9NQ90 (Human polyomavirus 9) Explore E9NQ90  Go to UniProtKB:  E9NQ90 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | E9NQ90 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | K, L, M, N, O K, L, M, N, O, P, Q, R, S | 3 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G00065MO GlyCosmos:  G00065MO GlyGen:  G00065MO |
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
EDO Query on EDO | AB [auth G] CA [auth B] DA [auth B] DB [auth H] EA [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
IPA Query on IPA | AA [auth A] BB [auth G] GA [auth B] HB [auth H] JA [auth C] | ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N | |||
CA Query on CA | BA [auth B] CB [auth H] HA [auth C] IB [auth I] KA [auth D] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900067 Query on PRD_900067 | K, L, M, N, O | 3'-sialyl-N-acetyllactosamine | Oligosaccharide / Substrate analog |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.213 
- R-Value Work: 0.179 
- R-Value Observed: 0.180 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 96.91 | α = 90 |
b = 180.63 | β = 90 |
c = 199.42 | γ = 90 |
Software Name | Purpose |
---|---|
RemDAq | data collection |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
Entry History 
Deposition Data
- Released Date: 2014-04-09  Deposition Author(s): Khan, Z.M., Stehle, T.
Revision History (Full details and data files)
- Version 1.0: 2014-04-09
Type: Initial release - Version 1.1: 2014-11-26
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-09-20
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary