8K4Z

Crystal structure of human MMP-7 in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8K4Z/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-07-20 Released: 2024-04-17 
• Deposition Author(s): Kamitani, M., Mima, M., Oka, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.239 
• R-Value Work: 0.203 

Literature

Discovery of TP0628103: A Selective MMP-7 Inhibitor Based on the Mitigation of OATP Substrate Recognition through Isoelectric Point Shift Strategy

Oka, Y., Abe-Sato, K., Tabuse, H., Yasukawa, Y., Yahara, T., Nishimoto, T., Kamitani, M., Fukunaga, T., Ochiai, N., Kumasaka-Abe, T., Hitaka, K., Gunji, E., Ohara, H., Takeda, T., Kojima, N., Asami, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 20.55 kDa 
• Atom Count: 1,409 
• Modelled Residue Count: 170 
• Deposited Residue Count: 181 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrilysin	A	175	Homo sapiens	Mutation(s): 1  Gene Names: MMP7, MPSL1, PUMP1 EC: 3.4.24.23
UniProt & NIH Common Fund Data Resources
Find proteins for P09237 (Homo sapiens) Explore P09237  Go to UniProtKB:  P09237
PHAROS:  P09237 GTEx:  ENSG00000137673

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Inhibitor	B	6	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	G [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
ZN	E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
N9P	B	L-PEPTIDE LINKING	C8 H10 N2 O2		ALA
TBG	B	L-PEPTIDE LINKING	C6 H13 N O2		VAL

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.239 
• R-Value Work: 0.203 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.799	α = 90
b = 75.799	β = 90
c = 60.53	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Kamitani, M., Mima, M., Oka, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release