Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 96.15 kDa 
• Atom Count: 6917 
• Residue Count: 815 
• Unique protein chains: 1

4DD8

ADAM-8 metalloproteinase domain with bound batimastat

• DOI: 10.2210/pdb4DD8/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2012-01-18 Released: 2012-06-06 
• Deposition Author(s): Hall, T., Shieh, H.S., Day, J.E., Caspers, N., Chrencik, J.E., Williams, J.M., Pegg, L.E., Pauley, A.M., Moon, A.F., Krahn, J.M., Fischer, D.H., Kiefer, J.R., Tomasselli, A.G., Zack, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.255 
• R-Value Work: 0.188 
• R-Value Observed: 0.192 

Literature

Structure of human ADAM-8 catalytic domain complexed with batimastat.

Hall, T., Shieh, H.S., Day, J.E., Caspers, N., Chrencik, J.E., Williams, J.M., Pegg, L.E., Pauley, A.M., Moon, A.F., Krahn, J.M., Fischer, D.H., Kiefer, J.R., Tomasselli, A.G., Zack, M.D.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 616-621

• PubMed: 22684055 
• DOI: 10.1107/S1744309112015618
• Primary Citation of Related Structures:  
  4DD8


• PubMed Abstract: 
  

The role of ADAM-8 in cancer and inflammatory diseases such as allergy, arthritis and asthma makes it an attractive target for drug development. Therefore, the catalytic domain of human ADAM-8 was expressed, purified and crystallized in complex with a hydroxamic acid inhibitor, batimastat. The crystal structure of the enzyme-inhibitor complex was refined to 2.1 Å resolution. ADAM-8 has an overall fold similar to those of other ADAM members, including a central five-stranded β-sheet and a catalytic Zn(2+) ion. However, unique differences within the S1' binding loop of ADAM-8 are observed which might be exploited to confer specificity and selectivity to ADAM-8 competitive inhibitors for the treatment of diseases involving this enzyme.

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Organizational Affiliation: 

Pfizer Inc, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disintegrin and metalloproteinase domain-containing protein 8	A, B, C, D	208	Homo sapiens	Mutation(s): 0  Gene Names: ADAM8, MS2 EC: 3.4.24
Find proteins for P78325 (Homo sapiens) Explore P78325  Go to UniProtKB:  P78325
NIH Common Fund Data Resources
PHAROS:  P78325 GTEx:  ENSG00000151651

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BAT	A, B, C, D	4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE C23 H31 N3 O4 S2 XFILPEOLDIKJHX-QYZOEREBSA-N
ZN	A, B, C, D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A, B, C, D	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K	A	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	A, B, C, D	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	A, B, C, D	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.255 
• R-Value Work: 0.188 
• R-Value Observed: 0.192 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.6	α = 90
b = 50.9	β = 102.4
c = 93.5	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
PHENIX	refinement
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-18 
• Released Date: 2012-06-06 
Deposition Author(s): Hall, T., Shieh, H.S., Day, J.E., Caspers, N., Chrencik, J.E., Williams, J.M., Pegg, L.E., Pauley, A.M., Moon, A.F., Krahn, J.M., Fischer, D.H., Kiefer, J.R., Tomasselli, A.G., Zack, M.D.

Revision History 

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2012-06-27
  Changes: Database references