1GPF | pdb_00001gpf

CHITINASE B FROM SERRATIA MARCESCENS IN COMPLEX WITH INHIBITOR PSAMMAPLIN

• PDB DOI: https://doi.org/10.2210/pdb1GPF/pdb

• Classification: HYDROLASE
• Organism(s): Serratia marcescens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-11-03 Released: 2002-10-31 
• Deposition Author(s): Komander, D., Van Aalten, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.245 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Psammaplin A, a Chitinase Inhibitor Isolated from the Fijian Marine Sponge Aplysinella Rhax

Tabudravu, J.N., Eijsink, V.G., Gooday, G.W., Jaspars, M., Komander, D., Legg, M., Synstad, B., Van Aalten, D.M.

(2002) Bioorg Med Chem 10: 1123

• PubMed: 11836123 
• DOI: https://doi.org/10.1016/s0968-0896(01)00372-8
• Primary Citation Related Structures: 
  1GPF


• PubMed Abstract: 
  

  Several brominated tyrosine derived compounds, psammaplins A (1), K (2) and L (3) as well as bisaprasin (4) were isolated from the Fijian marine sponge Aplysinella rhax during a bioassay guided isolation protocol. Their structures were determined using NMR and MS techniques. Psammaplin A was found to moderately inhibit chitinase B from Serratia marcescens, the mode of inhibition being non-competitive. Crystallographic studies suggest that a disordered psammaplin A molecule is bound near the active site. Interestingly, psammaplin A was found to be a potent antifungal agent.

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Organizational Affiliation: 
• Marine Natural Products Laboratory, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 111.32 kDa 
• Atom Count: 8,460 
• Modeled Residue Count: 994 
• Deposited Residue Count: 998 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHITINASE B	A, B	499	Serratia marcescens	Mutation(s): 0  EC: 3.2.1.14
UniProt
Find proteins for Q54276 (Serratia marcescens) Explore Q54276  Go to UniProtKB:  Q54276

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.245 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.754	α = 90
b = 103.588	β = 90
c = 186.065	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-31 
Deposition Author(s): Komander, D., Van Aalten, D.M.

Revision History  

• Version 1.0: 2002-10-31
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-10-09
  Changes: Advisory, Data collection, Experimental preparation, Other
• Version 1.4: 2023-12-13
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.5: 2024-10-23
  Changes: Structure summary