1LLO | pdb_00001llo

HEVAMINE A (A PLANT ENDOCHITINASE/LYSOZYME) COMPLEXED WITH ALLOSAMIDIN

• PDB DOI: https://doi.org/10.2210/pdb1LLO/pdb

• Classification: HYDROLASE
• Organism(s): Hevea brasiliensis
• Mutation(s): No 


• Deposited: 1995-11-08 Released: 1996-03-08 
• Deposition Author(s): Terwisscha Van Scheltinga, A.C., Armand, S., Kalk, K.H., Isogai, A., Henrissat, B., Dijkstra, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.200 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.292 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Literature

Stereochemistry of chitin hydrolysis by a plant chitinase/lysozyme and X-ray structure of a complex with allosamidin: evidence for substrate assisted catalysis.

Terwisscha van Scheltinga, A.C., Armand, S., Kalk, K.H., Isogai, A., Henrissat, B., Dijkstra, B.W.

(1995) Biochemistry 34: 15619-15623

• PubMed: 7495789 
• DOI: https://doi.org/10.1021/bi00048a003
• Primary Citation Related Structures: 
  1LLO


• PubMed Abstract: 
  

  The plant enzyme hevamine has both chitinase and lysozyme activity. HPLC analysis of the products of the hydrolysis of chitopentaose shows that hevamine acts with retention of the configuration, despite the absence of a nucleophilic or stabilizing carboxylate. To analyze the stabilization of a putative oxocarbonium ion intermediate, the X-ray structure of hevamine complexed with the inhibitor allosamidin was determined at 1.85 A resolution. This structure supports the role of Glu127 as a proton donor. The allosamizoline group binds in the center of the active site, mimicking a reaction intermediate in which a positive charge at C1 is stabilized intramolecularly by the carbonyl oxygen of the N-acetyl group at C2.

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Organizational Affiliation: 
• BIOSON Research Institute, University of Groningen, The Netherlands.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.21 kDa 
• Atom Count: 2,319 
• Modeled Residue Count: 273 
• Deposited Residue Count: 273 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hevamine-A	A	273	Hevea brasiliensis	Mutation(s): 0  EC: 3.2.1.14 (PDB Primary Data), 3.2.1.17 (PDB Primary Data)
UniProt
Find proteins for P23472 (Hevea brasiliensis) Explore P23472  Go to UniProtKB:  P23472

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G77950XB GlyCosmos: G77950XB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMI	C [auth B]	ALLOSAMIZOLINE C9 H16 N2 O4 MKJAYSJDHSEFRI-PVFLNQBWSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000468	B	Allosamidin	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.200 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.292 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.33	α = 90
b = 57.99	β = 90
c = 82.25	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-03-08 
Deposition Author(s): Terwisscha Van Scheltinga, A.C., Armand, S., Kalk, K.H., Isogai, A., Henrissat, B., Dijkstra, B.W.

Revision History  

• Version 1.0: 1996-03-08
  Type: Initial release
  
• Version 1.1: 2008-03-03
  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: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.0: 2022-03-09
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 4.0: 2022-06-01
  Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 4.1: 2024-10-30
  Changes: Data collection, Structure summary