Macromolecule Content

Total Structure Weight: 36528.33
Atom Count: 2615
Residue Count: 318
Unique protein chains: 1

6ENM

Crystal structure of MMP12 in complex with hydroxamate inhibitor LP168.

DOI: 10.2210/pdb6ENM/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): 1

Deposited: 2017-10-05 Released: 2018-05-16
Deposition Author(s): Vera, L., Nuti, E., Rossello, A., Stura, E.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.202
R-Value Work: 0.174

wwPDB Validation3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Development of Thioaryl-Based Matrix Metalloproteinase-12 Inhibitors with Alternative Zinc-Binding Groups: Synthesis, Potentiometric, NMR, and Crystallographic Studies.

Nuti, E., Cuffaro, D., Bernardini, E., Camodeca, C., Panelli, L., Chaves, S., Ciccone, L., Tepshi, L., Vera, L., Orlandini, E., Nencetti, S., Stura, E.A., Santos, M.A., Dive, V., Rossello, A.

(2018) J. Med. Chem. 61: 4421-4435

PubMed: 29727184 Search on PubMed
Primary Citation of Related Structures:
6ESM, 6EOX, 6ELA, 6EKN

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Macrophage metalloelastase	A, B	159	Homo sapiens	Mutation(s): 1 Gene Names: MMP12 (HME) EC: 3.4.24.65
Find proteins for P39900 (Homo sapiens) Go to Gene View: MMP12 Go to UniProtKB: P39900
Protein Feature View Full Protein Feature View for P39900

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
ZN Query on ZN Download SDF File Download CCD File	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
CA Query on CA Download SDF File Download CCD File	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction
LPW Query on LPW Download SDF File Download CCD File	A, B	2-[2-[4-(4-methoxyphenyl)phenyl]sulfonylphenyl]-~{N}-oxidanyl-ethanamide C₂₁ H₁₉ N O₅ S DJZNIZCARKSSDE-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.202
R-Value Work: 0.174
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 61.410	α = 90.00
b = 67.090	β = 90.00
c = 68.440	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

Deposited Date: 2017-10-05
Released Date: 2018-05-16
Deposition Author(s): Vera, L., Nuti, E., Rossello, A., Stura, E.A.

Revision History

Version 1.0: 2018-05-16
Type: Initial release
Version 1.1: 2018-06-06
Type: Data collection, Database references

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