Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 18817.20 
• Atom Count: 1346 
• Residue Count: 166 
• Unique protein chains: 2

1I73

COMPLEX OF PRO-LEU-L-TRP PHOSPHONATE WITH THE CATALITIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM)

• DOI: 10.2210/pdb1I73/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2001-03-07 Released: 2001-03-21 
• Deposition Author(s): Gavuzzo, E., Pochetti, G., Mazza, F., Gallina, C., Gorini, B., D'Alessio, S., Pieper, M., Tschesche, H., Tucker, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.4 Å
• R-Value Free: 0.194 
• R-Value Work: 0.134 

Literature

Two crystal structures of human neutrophil collagenase, one complexed with a primed- and the other with an unprimed-side inhibitor: implications for drug design.

Gavuzzo, E., Pochetti, G., Mazza, F., Gallina, C., Gorini, B., D'Alessio, S., Pieper, M., Tschesche, H., Tucker, P.A.

(2000) J.Med.Chem. 43: 3377-3385

• PubMed: 10978185 
• Primary Citation of Related Structures:  
  1I76
• Also Cited By: 1ZVX, 1ZS0


• PubMed Abstract: 
  

Two crystal structures of human neutrophil collagenase (HNC, MMP-8), one complexed with a primed- and the other with an unprimed-side inhibitor, were determined using synchrotron radiation at 100 K. Both inhibitors contain non-hydroxamate zinc-binding functions. The Pro-Leu-L-Trp(P)(OH)(2) occupies the unprimed region of the active site, furnishes new structural information regarding interaction between the catalytic zinc ion and the phosphonate group, and is the only example of occupation of the S(1) subsite of MMP-8 by the bulky tryptophan side chain. The (R)-2-(biphenyl-4-ylsulfonyl)-1,2,3, 4-tetrahydroisochinolin-3-carboxylic acid, a conformationally constrained D-Tic derivative, accommodates its biphenyl substituent into the deep primary specificity S(1)' subsite, inducing a widening of the entrance to this pocket; this modification of the protein, mainly consisting in a shift of the segment centered at Pro217, is observed for the first time in MMP-8 complexes. Cation-aromatic interactions can stabilize the formation of both complexes, and the beneficial effect of aromatic substituents in proximity of the catalytic zinc ion is discussed. The phosphonate group bound to either a primed- or unprimed-side inhibitor maintains the same relative position with respect to the catalytic zinc ion, suggesting that this binding function can be exploited for the design of combined inhibitors assembled to interact with both primed and unprimed regions of the active cleft.

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Related Citations: 

• Quantitative Structure-Activity Relationship of Human Neutrophil Collagenase (Mmp8-8) Inhibitors Using Comparative Molecular Field Analysis and X-Ray Structure Analysis
  Matter, H.,Schwab, W.,Barbier, D.,Billen, G.,Haase, B.,Neises, B.,Schudok, M.,Thorwart, W.,Schreuder, H.,Brachvogel, V.,Loenze, P.,Weithmann, K.U.
  (1999) J.Med.Chem. 42: 1908
• X-RAY STRUCTURES OF HUMAN NEUTROPHIL COLLAGENASE COMPLEXED WITH PEPTIDE HYDROXAMATE AND PEPTIDE THIOL INHIBITORS. IMPLICATIONS FOR SUBSTRATE BINDING AND RATIONAL DRUG DESIGN
  Grams, F.,Reinemer, P.,Powers, J.C.,Kleine, T.,Pieper, M.,Tschesche, H.,Huber, R.,Bode, W.
  (1995) Eur.J.Biochem. 228: 830




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Organizational Affiliation: 

Istituto di Strutturistica Chimica, CNR, C. P. n. 10, 00016 Monterotondo Stazione, Roma, Italy.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NEUTROPHIL COLLAGENASE	A	163	Homo sapiens	Mutation(s): 0  Gene Names: MMP8 (CLG1) EC: 3.4.24.34
Find proteins for P22894 (Homo sapiens) Go to Gene View: MMP8 Go to UniProtKB:  P22894

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
THREE RESIDUE PEPTIDE INHIBITOR	B	3	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PAT	B	L-PEPTIDE LINKING	C11 H13 N2 O5 P		TRP

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.4 Å
• R-Value Free: 0.194 
• R-Value Work: 0.134 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 32.983	α = 90.00
b = 68.673	β = 90.00
c = 70.486	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-03-07 
• Released Date: 2001-03-21 
• Deposition Author(s): Gavuzzo, E., Pochetti, G., Mazza, F., Gallina, C., Gorini, B., D'Alessio, S., Pieper, M., Tschesche, H., Tucker, P.A.

Revision History 

• Version 1.0: 2001-03-21
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2017-10-04
  Type: Refinement description