2W0D

Does a Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases.

Structural Biology Knowledgebase: 2W0D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.179

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2W0D

Classification: HYDROLASE

Total Structure Weight: 76338.25

Macromolecule Entities
Molecule Chains Length Organism Details
MACROPHAGE METALLOELASTASE A, B, C, D 164 Homo sapiens EC#: 3.4.24.65 IUBMB
Fragment: CATALYTIC DOMAIN, RESIDUES 106-263
Mutation: E219A
Details: COMPOUND EXPRESSED WITH A 5XHIS TAG AT THE C-TERMINUS FOR CLONING/PURIFICATION PURPOSES
Gene Name(s): MMP12 Gene View HME
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CGS
Query on CGS

A, B, C, D N-HYDROXY-2(R)-[[(4-METHOXYPHENYL)SULFONYL](3- PICOLYL)AMINO]-3-METHYLBUTANAMIDE HYDROCHLORIDE
CGS-27023A (Synonym)
C18 H23 N3 O5 S
BSIZUMJRKYHEBR-QGZVFWFLSA-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)
ACT
Query on ACT

A, C, D ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
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)
CL
Query on CL

C, D CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

D SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CGS N/A in BindingDB
IC50: 2 nM  BindingMOAD
IC50: 2.0 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.179
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 38.16 α = 90.00
b = 99.94 β = 96.59
c = 79.42 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-08-13
  • Released Date: 2009-03-03
  • Deposition author(s): Isaksson, J., Nystrom, S., Derbyshire, D.J., Wallberg, H., Agback, T., Kovacs, H., Bertini, I., Felli, I.C.

Revision History

  • 2011-12-28
    Type: Other | Details: Biological assembly, Sequence database correspondence, Citation, Refinement description
  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4
  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group