4AIG | pdb_00004aig

ADAMALYSIN II WITH PHOSPHONATE INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb4AIG/pdb

• Classification: METALLOENDOPEPTIDASE
• Organism(s): Crotalus adamanteus
• Mutation(s): No 


• Deposited: 1997-10-16 Released: 1998-11-11 
• Deposition Author(s): Pochetti, G., Mazza, F., Gavuzzo, E., Cirilli, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 
  0.177 (Depositor) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

2 angstrom X-ray structure of adamalysin II complexed with a peptide phosphonate inhibitor adopting a retro-binding mode.

Cirilli, M., Gallina, C., Gavuzzo, E., Giordano, C., Gomis-Ruth, F.X., Gorini, B., Kress, L.F., Mazza, F., Paradisi, M.P., Pochetti, G., Politi, V.

(1997) FEBS Lett 418: 319-322

• PubMed: 9428736 
• DOI: https://doi.org/10.1016/s0014-5793(97)01401-4
• Primary Citation of Related Structures:  
  4AIG


• PubMed Abstract: 
  

  The search of reprolysin inhibitors offers the possibility of intervention against both matrixins and ADAMs. Here we report the crystal structure of the complex between adamalysin II, a member of the reprolysin family, and a phosphonate inhibitor modeled on an endogenous venom tripeptide. The inhibitor occupies the primed region of the cleavage site adopting a retro-binding mode. The phosphonate group ligates the zinc ion in an asymmetric bidentate mode and the adjacent Trp indole system partly fills the primary specificity subsite S1'. An adamalysin-based model of tumor necrosis factor-alpha-converting enzyme (TACE) reveals a smaller S1' pocket for this enzyme.

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Organizational Affiliation: 

Ist. Strutturistica Chimica, CNR, Rome, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.59 kDa 
• Atom Count: 1,840 
• Modelled Residue Count: 201 
• Deposited Residue Count: 201 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADAMALYSIN II	A	201	Crotalus adamanteus	Mutation(s): 0  EC: 3.4.24.46
UniProt
Find proteins for P34179 (Crotalus adamanteus) Explore P34179  Go to UniProtKB:  P34179

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLX	D [auth A]	N-[(FURAN-2-YL)CARBONYL]-(S)-LEUCYL-(R)-[1-AMINO-2(1H-INDOL-3-YL)ETHYL]-PHOSPHONIC ACID C21 H26 N3 O6 P WHPKSASOSKNDPY-PKOBYXMFSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work:  0.177 (Depositor) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.5	α = 90
b = 73.5	β = 90
c = 96.9	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
CCP4	data reduction
X-PLOR	model building
X-PLOR	refinement
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-11-11 
Deposition Author(s): Pochetti, G., Mazza, F., Gavuzzo, E., Cirilli, M.

Revision History  

• Version 1.0: 1998-11-11
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Data collection, Structure summary