Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47595.51 
• Atom Count: 3185 
• Residue Count: 425 
• Unique protein chains: 1

1L6J

Crystal structure of human matrix metalloproteinase MMP9 (gelatinase B).

• DOI: 10.2210/pdb1L6J/pdb

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


• Deposited: 2002-03-11 Released: 2002-07-03 
• Deposition Author(s): Elkins, P.A., Ho, Y.S., Smith, W.W., Janson, C.A., D'Alessio, K.J., McQueney, M.S., Cummings, M.D., Romanic, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.230 
• R-Value Work: 0.187 

Literature

Structure of the C-terminally truncated human ProMMP9, a gelatin-binding matrix metalloproteinase.

Elkins, P.A., Ho, Y.S., Smith, W.W., Janson, C.A., D'Alessio, K.J., McQueney, M.S., Cummings, M.D., Romanic, A.M.

(2002) Acta Crystallogr.,Sect.D 58: 1182-1192

• PubMed: 12077439 


• PubMed Abstract: 
  

The X-ray crystal structure of the proform of human matrix metalloproteinase MMP9 has been solved to 2.5 A resolution. The construct includes the prodomain, the catalytic domain and three FnII (fibronectin type II) domains. The prodomain is inserted into the active-site cleft, blocking access to the catalytic zinc. Comparison with the crystal structure of the most closely related MMP, MMP2, indicates that the conformations of residues in the active-site cleft and in the cysteine-switch peptide of the prodomain are highly conserved and that design of MMP9-specific inhibitors will be challenging. In common with MMP2, the MMP9 S1' inhibitor-binding pocket is large compared with that of other MMPs. One small point of difference in the S1' binding pockets of MMP9 and MMP2 may provide an opportunity to explore the design of specific inhibitors. The side chain of Arg424 in MMP9 is angled slightly away from the S1' pocket when compared with the corresponding residue in MMP2, Thr424. The secondary structure of the FnII domains is conserved between the two closely related MMPs, although the second FnII domain makes no contact with the catalytic domain in MMP9, while the same domain in MMP2 has a substantial area of interaction with the catalytic domain.

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Organizational Affiliation: 

GlaxoSmithKline, King of Prussia, Pennsylvania 19406, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Matrix metalloproteinase-9	A	425	Homo sapiens	Mutation(s): 0  Gene Names: MMP9 (CLG4B) EC: 3.4.24.35
Find proteins for P14780 (Homo sapiens) Go to Gene View: MMP9 Go to UniProtKB:  P14780

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.230 
• R-Value Work: 0.187 
• Space Group: P 6₅

Unit Cell:

Length (Å)	Angle (°)
a = 123.685	α = 90.00
b = 123.685	β = 90.00
c = 89.937	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-03-11 
• Released Date: 2002-07-03 
• Deposition Author(s): Elkins, P.A., Ho, Y.S., Smith, W.W., Janson, C.A., D'Alessio, K.J., McQueney, M.S., Cummings, M.D., Romanic, A.M.

Revision History 

• Version 1.0: 2002-07-03
  Type: Initial release
• Version 1.1: 2008-04-28
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance