4H82

Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor.

Structural Biology Knowledgebase: 4H82 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.207

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4H82

Classification: hydrolase / hydrolase inhibitor

Total Structure Weight: 75699.61

Macromolecule Entities
Molecule Chains Length Organism Details
Matrix metalloproteinase-9 A, B, C, D 160 Homo sapiens EC#: 3.4.24.35 IUBMB
Fragment: MMP-9 catalytic domain 107-215,391-444
Mutation: E227Q
Gene Name(s): MMP9 Gene View CLG4B
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
L29
Query on L29

A, D N,N'-bis(2-{(biphenyl-4-ylsulfonyl)[(2R)- 1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]amino}ethyl)benzene- 1,3-dicarboxamide (non-preferred name)
C46 H52 N6 O10 S2
JPMXJRBHCOULJI-NCRNUEESSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

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

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

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

C PROPANOIC ACID
C3 H6 O2
XBDQKXXYIPTUBI-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.207
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 39.90 α = 90.03
b = 98.86 β = 111.95
c = 47.13 γ = 89.98

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-21
  • Released Date: 2013-05-01
  • Deposition author(s): Antoni, C., Stura, E.A., Vera, L., Cassar-Lajeunesse, E., Nuti, E., Dive, V., Rossello, A.

Revision History

  • 2015-08-12
    Type: Citation | Details: Citation update
  • 2014-10-15
    Type: Biological assembly | Details: --
  • 2014-10-08
    Type: Citation | Details: --