1EAK

Catalytic domain of proMMP-2 E404Q mutant

• PDB DOI: https://doi.org/10.2210/pdb1EAK/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Trichoplusia ni
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2001-07-12 Released: 2002-08-22 
• Deposition Author(s): Bergmann, U., Tuuttila, A., Tryggvason, K., Morgunova, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.303 
• R-Value Work: 0.271 
• R-Value Observed: 0.271 

Literature

Crystal Structure of Human Mmp-2 Reveals a New P

Bergmann, U., Tuuttila, A., Morgunova, E., Tryggvason, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 191.88 kDa 
• Atom Count: 13,504 
• Modelled Residue Count: 1,693 
• Deposited Residue Count: 1,700 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
72 KDA TYPE IV COLLAGENASE	A, B, C, D	421	Homo sapiens	Mutation(s): 1  EC: 3.4.24.24 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P08253 (Homo sapiens) Explore P08253  Go to UniProtKB:  P08253
PHAROS:  P08253 GTEx:  ENSG00000087245

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
INHIBITOR PEPTIDE	E [auth P], F [auth R]	8	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], L [auth B], M [auth B], R [auth C], S [auth C], X [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	H [auth A], I [auth A], N [auth B], O [auth B], T [auth C], U [auth C], Y [auth D], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	AA [auth D], BA [auth D], J [auth A], K [auth A], P [auth B], Q [auth B], V [auth C], W [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.303 
• R-Value Work: 0.271 
• R-Value Observed: 0.271 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.67	α = 90
b = 166.15	β = 90
c = 170.13	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
ROTAPREP	data scaling
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-08-22 
Deposition Author(s): Bergmann, U., Tuuttila, A., Tryggvason, K., Morgunova, E.

Revision History  

• Version 1.0: 2002-08-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2016-12-21
  Changes: Source and taxonomy
• Version 1.3: 2018-06-13
  Changes: Data collection
• Version 1.4: 2019-04-03
  Changes: Data collection, Source and taxonomy
• Version 1.5: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description