4MBY
Structure of B-Lymphotropic Polyomavirus VP1 in complex with 3'-sialyllactose
- PDB DOI: https://doi.org/10.2210/pdb4MBY/pdb
- Classification: VIRAL PROTEIN
- Organism(s): B-lymphotropic polyomavirus
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No 
- Deposited: 2013-08-21 Released: 2013-12-04 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.48 Å
- R-Value Free: 0.186 
- R-Value Work: 0.165 
- R-Value Observed: 0.166 
wwPDB Validation   3D Report Full Report
This is version 2.2 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 |
Major Capsid Protein VP1 | 278 | B-lymphotropic polyomavirus | Mutation(s): 0  Gene Names: VP1 | ||
UniProt | |||||
Find proteins for P04010 (B-lymphotropic polyomavirus) Explore P04010  Go to UniProtKB:  P04010 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P04010 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
EDO Query on EDO | AB [auth E] AC [auth J] BC [auth J] DA [auth B] EA [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
IPA Query on IPA | AA [auth A] BB [auth E] CC [auth J] FB [auth F] JA [auth B] | ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N | |||
CA Query on CA | BA [auth B] CB [auth F] GB [auth G] KA [auth C] LB [auth H] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
CL Query on CL | CA [auth B] DB [auth F] HB [auth G] LA [auth C] MB [auth H] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.48 Å
- R-Value Free: 0.186 
- R-Value Work: 0.165 
- R-Value Observed: 0.166 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 150.53 | α = 90 |
b = 97.21 | β = 96.25 |
c = 234.66 | γ = 90 |
Software Name | Purpose |
---|---|
RemDAq | data collection |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
Entry History 
Deposition Data
- Released Date: 2013-12-04  Deposition Author(s): Khan, Z.M., Neu, U., Stehle, T.
Revision History (Full details and data files)
- Version 1.0: 2013-12-04
Type: Initial release - Version 1.1: 2014-01-22
Changes: Source and taxonomy - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-02-28
Changes: Data collection, Database references, Structure summary - Version 2.2: 2024-04-03
Changes: Refinement description