Crystal structure of human MMP1 catalytic domain at 2.2 A resolution

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.215 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


The catalytic domain of MMP-1 studied through tagged lanthanides.

Bertini, I.Calderone, V.Cerofolini, L.Fragai, M.Geraldes, C.F.Hermann, P.Luchinat, C.Parigi, G.Teixeira, J.M.

(2012) FEBS Lett 586: 557-567

  • DOI: https://doi.org/10.1016/j.febslet.2011.09.020
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Pseudocontact shifts (pcs) and paramagnetic residual dipolar couplings (rdc) provide structural information that can be used to assess the adequacy of a crystallographic structure to represent the solution structure of a protein. This can be done by attaching a lanthanide binding tag to the protein. There are cases in which only local rearrangements are sufficient to match the NMR data and cases where significant secondary structure or domain rearrangements from the solid state to the solution state are needed. We show that the two cases are easily distinguishable. Whereas the use of solution restraints in the latter case is described in the literature, here we deal with how to obtain a better model of the solution structure in a case (the catalytic domain of the matrix metalloproteinase MMP-1) of the former class.

  • Organizational Affiliation

    Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy. ivanobertini@cerm.unifi.it

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interstitial collagenaseA,
B [auth G],
C [auth M]
156Homo sapiensMutation(s): 0 
Gene Names: MMP1CLG
UniProt & NIH Common Fund Data Resources
Find proteins for P03956 (Homo sapiens)
Explore P03956 
Go to UniProtKB:  P03956
GTEx:  ENSG00000196611 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03956
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
I [auth G]
J [auth G]
N [auth M]
D [auth A],
E [auth A],
I [auth G],
J [auth G],
N [auth M],
O [auth M]
Query on CA

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
K [auth G]
L [auth G]
F [auth A],
G [auth A],
H [auth A],
K [auth G],
L [auth G],
M [auth G],
P [auth M],
Q [auth M],
R [auth M]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.694α = 90
b = 54.528β = 120.69
c = 94.905γ = 90
Software Package:
Software NamePurpose
CrysalisProdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-10-12
    Changes: Database references
  • Version 1.2: 2012-03-21
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description