5LAB | pdb_00005lab

Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor NNGH

• PDB DOI: https://doi.org/10.2210/pdb5LAB/pdb

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


• Deposited: 2016-06-14 Released: 2016-08-10 
• Deposition Author(s): Ravera, E., Calderone, V., Luchinat, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 
  0.195 (Depositor) 
• R-Value Work: 
  0.155 (Depositor) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

First-principles calculation of pseudo-contact shifts in a paramagnetic metalloprotein

Benda, L., Mares, J., Ravera, E., Parigi, G., Luchinat, C., Kaupp, M., Vaara, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 18.18 kDa 
• Atom Count: 1,508 
• Modeled Residue Count: 159 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage metalloelastase	A	159	Homo sapiens	Mutation(s): 1  Gene Names: MMP12, HME EC: 3.4.24.65
UniProt & NIH Common Fund Data Resources
Find proteins for P39900 (Homo sapiens) Explore P39900  Go to UniProtKB:  P39900
PHAROS:  P39900 GTEx:  ENSG00000262406

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NGH	G [auth A]	N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID C13 H20 N2 O5 S JIRXORZYIXSWOB-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NGH	BindingDB:  5LAB	Ki: 4.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free:  0.195 (Depositor) 
• R-Value Work:  0.155 (Depositor) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.19	α = 90
b = 62.56	β = 90
c = 37.26	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Ravera, E., Calderone, V., Luchinat, C.

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2025-01-29
  Changes: Advisory, Structure summary