2VLC

Crystal structure of Natural Cinnamomin (Isoform III)

• PDB DOI: https://doi.org/10.2210/pdb2VLC/pdb

• Classification: HYDROLASE
• Organism(s): Cinnamomum camphora
• Mutation(s): No 


• Deposited: 2008-01-11 Released: 2009-02-10 
• Deposition Author(s): Azzi, A., Wang, T., Zhu, D.-W., Zou, Y.-S., Liu, W.-Y., Lin, S.-X.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.309 
• R-Value Work: 0.238 
• R-Value Observed: 0.242 

Literature

Crystal Structure of Native Cinnamomin Isoform III and its Comparison with Other Ribosome Inactivating Proteins.

Azzi, A., Wang, T., Zhu, D.-W., Zou, Y.-S., Liu, W.-Y., Lin, S.-X.

(2009) Proteins 74: 250

• PubMed: 18837036 
• DOI: https://doi.org/10.1002/prot.22251
• Primary Citation of Related Structures:  
  2VLC

---

Organizational Affiliation: 

Structural Biology Platform, Institute of Biochemistry and Cell Biology (IBCB), Shanghai Institutes of Biological Sciences (SIBS), Chinese Academy of Sciences, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 130.07 kDa 
• Atom Count: 8,406 
• Modelled Residue Count: 1,036 
• Deposited Residue Count: 1,140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome-inactivating protein	A, B	570	Cinnamomum camphora	Mutation(s): 0
UniProt
Find proteins for Q94BW3 (Cinnamomum camphora) Explore Q94BW3  Go to UniProtKB:  Q94BW3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, F, G, H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMA	I [auth A], L [auth B]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
XYP	J [auth A], K [auth B]	beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.309 
• R-Value Work: 0.238 
• R-Value Observed: 0.242 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.388	α = 90
b = 126.329	β = 90
c = 161.451	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-10 
Deposition Author(s): Azzi, A., Wang, T., Zhu, D.-W., Zou, Y.-S., Liu, W.-Y., Lin, S.-X.

Revision History  

• Version 1.0: 2009-02-10
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.0: 2022-12-07
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 4.0: 2023-09-27
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
• Version 4.1: 2024-01-31
  Changes: Refinement description