4I03

Human MMP12 in complex with a PEG-linked bifunctional L-glutamate motif inhibitor

Structural Biology Knowledgebase: 4I03 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.144

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4I03

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 19807.20

Macromolecule Entities
Molecule Chains Length Organism Details
Macrophage metalloelastase A 159 Homo sapiens EC#: 3.4.24.65 IUBMB
Fragment: catalytic domain (UNP residues 106-263)
Mutation: F171D, E219A
Gene Name(s): MMP12 Gene View HME

Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
L88
Query on L88

A (4R,22R)-5,21-dioxo-4,22-bis({3-[4-(4-phenylthiophen- 2-yl)phenyl]propanoyl}amino)-10,13,16-trioxa- 6,20-diazapentacosane-1,25-dioic acid
C58 H66 N4 O11 S2
PAOWMYIFDMOPGM-CDKYPKJRSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGO
Query on PGO

A S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.144
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 51.79 α = 90.00
b = 60.10 β = 116.67
c = 54.92 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-16
  • Released Date: 2013-04-24
  • Deposition author(s): Stura, E.A., Vera, L., Devel, L., Cassar-Lajeunesse, E., Dive, V.

Revision History

  • 2013-07-03
    Type: Citation | Details: Citation update