1CGL

Structure of the catalytic domain of fibroblast collagenase complexed with an inhibitor

PDB DOI: https://doi.org/10.2210/pdb1CGL/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 1993-11-17 Released: 1995-02-27
Deposition Author(s): Lovejoy, B., Cleasby, A., Hassell, A.M., Longley, K., Luther, M.A., Weigl, D., Mcgeehan, G., Mcelroy, A.B., Drewry, D., Lambert, M.H., Jordan, S.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Work: 0.186
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structure of the catalytic domain of fibroblast collagenase complexed with an inhibitor.

Lovejoy, B., Cleasby, A., Hassell, A.M., Longley, K., Luther, M.A., Weigl, D., McGeehan, G., McElroy, A.B., Drewry, D., Lambert, M.H., Jordan, S.R.

(1994) Science 263: 375-377

PubMed: 8278810 Search on PubMed
DOI: https://doi.org/10.1126/science.8278810
Primary Citation of Related Structures:
1CGL

PubMed Abstract:
Collagenase is a zinc-dependent endoproteinase and is a member of the matrix metalloproteinase (MMP) family of enzymes. The MMPs participate in connective tissue remodeling events and aberrant regulation has been associated with several pathologies. The 2.4 angstrom resolution structure of the inhibited enzyme revealed that, in addition to the catalytic zinc, there is a second zinc ion and a calcium ion which play a major role in stabilizing the tertiary structure of collagenase. Despite scant sequence homology, collagenase shares structural homology with two other endoproteinases, bacterial thermolysin and crayfish astacin. The detailed description of protein-inhibitor interactions present in the structure will aid in the design of compounds that selectively inhibit individual members of the MMP family. Such inhibitors will be useful in examining the function of MMPs in pathological processes.

Organizational Affiliation

Glaxo Research Institute, Research Triangle Park, NC 27709.

Macromolecule Content

Total Structure Weight: 39.41 kDa
Atom Count: 2,728
Modelled Residue Count: 325
Deposited Residue Count: 338
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FIBROBLAST COLLAGENASE	A, B	169	Homo sapiens	Mutation(s): 0 EC: 3.4.24.7
UniProt & NIH Common Fund Data Resources
Find proteins for P03956 (Homo sapiens) Explore P03956 Go to UniProtKB: P03956
PHAROS: P03956 GTEx: ENSG00000196611
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03956
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0ED Query on 0ED Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B]	F [auth A], J [auth B]	N-[(1S)-3-{[(benzyloxy)carbonyl]amino}-1-carboxypropyl]-L-leucyl-N-(2-morpholin-4-ylethyl)-L-phenylalaninamide C₃₃ H₄₇ N₅ O₇ XQSMAYNMHYYWCR-ULNSLHSMSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	C [auth A], D [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B]	E [auth A], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
0ED	Binding MOAD: 1CGL	Ki: 135 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000258 (0ED) Query on PRD_000258	F [auth A], J [auth B]	N-[(1S)-3-{[(benzyloxy)carbonyl]amino}-1-carboxypropyl]-L-leucyl-N-(2-morpholin-4-ylethyl)-L-phenylalaninamide	Peptide-like / Inhibitor		Interactions Focus chain F [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Work: 0.186
R-Value Observed: 0.186
Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.2	α = 90
b = 78.2	β = 90
c = 87.4	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1995-02-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1995-02-27
Type: Initial release
Version 1.1: 2008-05-22
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.3: 2012-12-12
Changes: Other
Version 1.4: 2019-11-20
Changes: Derived calculations, Other
Version 1.5: 2024-02-07
Changes: Data collection, Database references, Derived calculations