4H84

Crystal structure of the catalytic domain of Human MMP12 in complex with a selective carboxylate based inhibitor.

Structural Biology Knowledgebase: 4H84 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.171

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4H84

Classification: hydrolase / hydrolase inhibitor

Total Structure Weight: 38266.54

Macromolecule Entities
Molecule Chains Length Organism Details
Macrophage metalloelastase A, B 159 Homo sapiens EC#: 3.4.24.65 IUBMB
Fragment: Human MMP12 catalytic domain
Mutation: F171D
Gene Name(s): MMP12 Gene View HME

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
GOL
Query on GOL

A, B GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
PGO
Query on PGO

A, B S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
Ligand Explorer
 
JSmol
PGR
Query on PGR

A R-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-GSVOUGTGSA-N
Ligand Explorer
 
JSmol
Y38
Query on Y38

A, B N-[2-(benzoylamino)ethyl]-N-(biphenyl-4-ylsulfonyl)- D-valine
C26 H28 N2 O5 S
BKYHPXRQAHYJBN-XMMPIXPASA-N
Ligand Explorer
 
JSmol
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.171
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 42.14 α = 90.00
b = 62.79 β = 90.00
c = 113.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-21
  • Released Date: 2013-04-24
  • Deposition author(s): Stura, E.A., Antoni, C., Vera, L., Cassar-Lajeunesse, E., Nuti, E., Dive, V., Rossello, A.

Revision History

  • 2015-08-12
    Type: Citation | Details: Citation update
  • 2014-10-08
    Type: Entry authorship | Details: --