3GXZ
Crystal structure of cyanovirin-n complexed to oligomannose-9 (man-9)
- PDB DOI: https://doi.org/10.2210/pdb3GXZ/pdb
- Entry: 3GXZ supersedes: 1M5M
- Classification: ANTIVIRAL PROTEIN
- Organism(s): Nostoc ellipsosporum
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2009-04-03 Released: 2009-04-14 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.323 
- R-Value Work: 0.246 
- R-Value Observed: 0.250 
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 |
Cyanovirin-N | 101 | Nostoc ellipsosporum | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for P81180 (Nostoc ellipsosporum) Explore P81180  Go to UniProtKB:  P81180 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P81180 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 10 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G40702WU GlyCosmos:  G40702WU GlyGen:  G40702WU |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NHE Query on NHE | E [auth A] | 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N | |||
MG Query on MG | F [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.323 
- R-Value Work: 0.246 
- R-Value Observed: 0.250 
- Space Group: P 41 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 61.512 | α = 90 |
b = 61.512 | β = 90 |
c = 147.95 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
AMoRE | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
Entry History 
Deposition Data
- Released Date: 2009-04-14  Deposition Author(s): Botos, I., O'Keefe, B.R., Shenoy, S.R., Seeberger, P.H., Boyd, M.R., Wlodawer, A.
- This entry supersedes: 1M5M
Revision History (Full details and data files)
- Version 1.0: 2009-04-14
Type: Initial release - Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary