3SSB

Structure of Insect Metalloproteinase Inhibitor in Complex with Thermolysin

• PDB DOI: https://doi.org/10.2210/pdb3SSB/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Bacillus thermoproteolyticus, Galleria mellonella
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-07-08 Released: 2011-09-07 
• Deposition Author(s): Arolas, J.L., Botelho, T.O., Vilcinskas, A., Gomis-Ruth, F.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.193 
• R-Value Work: 0.159 
• R-Value Observed: 0.159 

Literature

Structural evidence for standard-mechanism inhibition in metallopeptidases from a complex poised to resynthesize a Peptide bond.

Arolas, J.L., Botelho, T.O., Vilcinskas, A., Gomis-Ruth, F.X.

(2011) Angew Chem Int Ed Engl 50: 10357-10360

• PubMed: 21915964 
• DOI: https://doi.org/10.1002/anie.201103262
• Primary Citation of Related Structures:  
  3SSB

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Organizational Affiliation: 

Proteolysis Lab, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Spain.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 85.36 kDa 
• Atom Count: 6,494 
• Modelled Residue Count: 760 
• Deposited Residue Count: 776 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermolysin	A, D [auth B]	316	Bacillus thermoproteolyticus	Mutation(s): 0  EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus) Explore P00800  Go to UniProtKB:  P00800

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Inducible metalloproteinase inhibitor protein	B [auth C], E [auth D]	40	Galleria mellonella	Mutation(s): 0  Gene Names: IMPI
UniProt
Find proteins for P82176 (Galleria mellonella) Explore P82176  Go to UniProtKB:  P82176

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Inducible metalloproteinase inhibitor protein	C [auth I], F [auth J]	32	Galleria mellonella	Mutation(s): 0  Gene Names: IMPI
UniProt
Find proteins for P82176 (Galleria mellonella) Explore P82176  Go to UniProtKB:  P82176

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], M [auth I], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	H [auth A], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	I [auth A], J [auth A], K [auth A], P [auth B], Q [auth B], R [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	L [auth A], S [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.193 
• R-Value Work: 0.159 
• R-Value Observed: 0.159 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.64	α = 90
b = 78.37	β = 90.08
c = 92.29	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-07 
Deposition Author(s): Arolas, J.L., Botelho, T.O., Vilcinskas, A., Gomis-Ruth, F.X.

Revision History  

• Version 1.0: 2011-09-07
  Type: Initial release
  
• Version 1.1: 2011-11-02
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description