1B5F
NATIVE CARDOSIN A FROM CYNARA CARDUNCULUS L.
- PDB DOI: https://doi.org/10.2210/pdb1B5F/pdb
- Classification: HYDROLASE
- Organism(s): Cynara cardunculus
- Mutation(s): No 
- Deposited: 1999-01-06 Released: 1999-01-13 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.72 Å
- R-Value Free: 0.256 
- R-Value Observed: 0.205 
wwPDB Validation   3D Report Full Report
This is version 3.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
PROTEIN (CARDOSIN A) | 239 | Cynara cardunculus | Mutation(s): 0  EC: 3.4.23 | ||
UniProt | |||||
Find proteins for Q9XFX3 (Cynara cardunculus) Explore Q9XFX3  Go to UniProtKB:  Q9XFX3 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9XFX3 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
PROTEIN (CARDOSIN A) | 87 | Cynara cardunculus | Mutation(s): 0  EC: 3.4.23 | ||
UniProt | |||||
Find proteins for Q9XFX3 (Cynara cardunculus) Explore Q9XFX3  Go to UniProtKB:  Q9XFX3 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9XFX3 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | E | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G17689EW GlyCosmos:  G17689EW GlyGen:  G17689EW |
Entity ID: 4 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | F, H | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G18638YB GlyCosmos:  G18638YB GlyGen:  G18638YB |
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | G | 6 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G43648DB GlyCosmos:  G43648DB GlyGen:  G43648DB |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.72 Å
- R-Value Free: 0.256 
- R-Value Observed: 0.205 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 116.964 | α = 90 |
b = 87.186 | β = 104.43 |
c = 81.303 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
SHELXL-97 | refinement |
Entry History 
Deposition Data
- Released Date: 1999-01-13  Deposition Author(s): Frazao, C., Bento, I., Carrondo, M.A.
Revision History (Full details and data files)
- Version 1.0: 1999-01-13
Type: Initial release - Version 1.1: 2007-10-16
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 3.0: 2020-09-23
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 3.1: 2023-08-09
Changes: Data collection, Database references, Refinement description