1AYK

INHIBITOR-FREE CATALYTIC FRAGMENT OF HUMAN FIBROBLAST COLLAGENASE, NMR, 30 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 30 
  • Selection Criteria: LOWEST ENERGY, LOWEST VIOLATIONS, CONSISTENT FOLD 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High-resolution solution structure of the inhibitor-free catalytic fragment of human fibroblast collagenase determined by multidimensional NMR.

Moy, F.J.Chanda, P.K.Cosmi, S.Pisano, M.R.Urbano, C.Wilhelm, J.Powers, R.

(1998) Biochemistry 37: 1495-1504

  • DOI: 10.1021/bi972181w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The high-resolution solution structure of the inhibitor-free catalytic fragment of human fibroblast collagenase (MMP-1), a protein of 18.7 kDa, which is a member of the matrix metalloproteinase family, has been determined using three-dimensional hete ...

    The high-resolution solution structure of the inhibitor-free catalytic fragment of human fibroblast collagenase (MMP-1), a protein of 18.7 kDa, which is a member of the matrix metalloproteinase family, has been determined using three-dimensional heteronuclear NMR spectroscopy. A total of 30 structures were calculated by means of hybrid distance geometry-simulated annealing using a total of 3333 experimental NMR restraints, consisting of 2409 approximate interproton distance restraints, 84 distance restraints for 42 backbone hydrogen bonds, 426 torsion angle restraints, 125 3JNH alpha restraints, 153 C alpha restraints, and 136 C beta restraints. The atomic rms distribution about the mean coordinate positions for the 30 structures for residues 7-137 and 145-163 is 0.42 +/- 0.04 A for the backbone atoms, 0.80 +/- 0.04 A for all atoms, and 0.50 +/- 0.03 A for all atoms excluding disordered side chains. The overall structure of MMP-1 is composed of a beta-sheet consisting of five beta-strands in a mixed parallel and anti-parallel arrangement and three alpha-helices. A best-fit superposition of the NMR structure of inhibitor-free MMP-1 with the 1.56 A resolution X-ray structure by Spurlino et al. [Spurlino, J. C., Smallwood, A. M., Carlton, D. D., Banks, T. M., Vavra, K. J., Johnson, J. S., Cook, E. R., Falvo, J., and Wahl, R. C., et al. (1994) Proteins: Struct., Funct., Genet. 19, 98-109] complexed with a hydroxamate inhibitor yields a backbone atomic rms difference of 1.22 A. The majority of differences between the NMR and X-ray structure occur in the vicinity of the active site for MMP-1. This includes an increase in mobility for residues 138-144 and a displacement for the Ca(2+)-loop (residues 74-80). Distinct differences were observed for side-chain torsion angles, in particular, the chi 1 for N80 is -60 degrees in the NMR structure compared to 180 degrees in the X-ray. This results in the side chain of N80 occupying and partially blocking access to the active site of MMP-1.


    Related Citations: 
    • Assignments, Secondary Structure and Dynamics of the Inhibitor-Free Catalytic Fragment of Human Fibroblast Collagenase
      Moy, F.J.,Pisano, M.R.,Chanda, P.K.,Urbano, C.,Killar, L.M.,Sung, M.-L.,Powers, R.
      (1997) J.Biomol.NMR 1: 9


    Organizational Affiliation

    Department of Structural Biology, Wyeth-Ayerst Research, Pearl River, New York 10965, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COLLAGENASE
A
169Homo sapiensMutation(s): 0 
Gene Names: MMP1 (CLG)
EC: 3.4.24.7
Find proteins for P03956 (Homo sapiens)
Go to Gene View: MMP1
Go to UniProtKB:  P03956
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 30 
  • Selection Criteria: LOWEST ENERGY, LOWEST VIOLATIONS, CONSISTENT FOLD 
  • Olderado: 1AYK Olderado
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-11-06 
  • Released Date: 1998-02-25 
  • Deposition Author(s): Powers, R., Moy, F.J.

Revision History 

  • Version 1.0: 1998-02-25
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance