5W1X
Crystal Structure of Humanpapillomavirus18 (HPV18) Capsid L1 Pentamers Bound to Heparin Oligosaccharides
- PDB DOI: https://doi.org/10.2210/pdb5W1X/pdb
- Entry: 5W1X supersedes: 3OFL
- Classification: VIRAL PROTEIN
- Organism(s): human papillomavirus 18
- Expression System: Escherichia coli
- Mutation(s): Yes 
- Deposited: 2017-06-05 Released: 2018-12-12 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.37 Å
- R-Value Free: 0.234 
- R-Value Work: 0.171 
- R-Value Observed: 0.174 
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 |
Major capsid protein L1 | 427 | human papillomavirus 18 | Mutation(s): 3  Gene Names: L1 | ||
UniProt | |||||
Find proteins for P06794 (Human papillomavirus type 18) Explore P06794  Go to UniProtKB:  P06794 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P06794 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose | AA [auth a], DA [auth d], IA [auth i], JA [auth j], KA [auth k], AA [auth a], DA [auth d], IA [auth i], JA [auth j], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], P, QA [auth q], RA [auth r], S, SA [auth s], T, U, W, Y, Z | 2 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G75183WV GlyCosmos:  G75183WV |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose | BA [auth b], CA [auth c], GA [auth g], HA [auth h], PA [auth p], BA [auth b], CA [auth c], GA [auth g], HA [auth h], PA [auth p], Q, R, V, X | 4 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G12683PR GlyCosmos:  G12683PR |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose | EA [auth e] | 6 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G29325GF GlyCosmos:  G29325GF |
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose | FA [auth f] | 10 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G59499PQ GlyCosmos:  G59499PQ |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.37 Å
- R-Value Free: 0.234 
- R-Value Work: 0.171 
- R-Value Observed: 0.174 
- Space Group: P 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 80.993 | α = 88.46 |
b = 106.49 | β = 85.75 |
c = 237.661 | γ = 69.02 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2018-12-12  Deposition Author(s): Chen, X.S., Dasgupta, J.
- This entry supersedes: 3OFL
Revision History (Full details and data files)
- Version 1.0: 2018-12-12
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary