2RJQ | pdb_00002rjq

Crystal structure of ADAMTS5 with inhibitor bound

• PDB DOI: https://doi.org/10.2210/pdb2RJQ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2007-10-15 Released: 2007-12-11 
• Deposition Author(s): Mosyak, L., Stahl, M., Somers, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.260 (Depositor) 
• R-Value Work: 
  0.230 (Depositor) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of the two major aggrecan degrading enzymes, ADAMTS4 and ADAMTS5.

Mosyak, L., Georgiadis, K., Shane, T., Svenson, K., Hebert, T., McDonagh, T., Mackie, S., Olland, S., Lin, L., Zhong, X., Kriz, R., Reifenberg, E.L., Collins-Racie, L.A., Corcoran, C., Freeman, B., Zollner, R., Marvell, T., Vera, M., Sum, P.E., Lavallie, E.R., Stahl, M., Somers, W.

(2008) Protein Sci 17: 16-21

• PubMed: 18042673 
• DOI: https://doi.org/10.1110/ps.073287008
• Primary Citation Related Structures: 
  2RJP, 2RJQ, 3B2Z


• PubMed Abstract: 
  

  Aggrecanases are now believed to be the principal proteinases responsible for aggrecan degradation in osteoarthritis. Given their potential as a drug target, we solved crystal structures of the two most active human aggrecanase isoforms, ADAMTS4 and ADAMTS5, each in complex with bound inhibitor and one wherein the enzyme is in apo form. These structures show that the unliganded and inhibitor-bound enzymes exhibit two essentially different catalytic-site configurations: an autoinhibited, nonbinding, closed form and an open, binding form. On this basis, we propose that mature aggrecanases exist as an ensemble of at least two isomers, only one of which is proteolytically active.

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Organizational Affiliation: 
• Department of Chemical and Screening Sciences, Wyeth Research, Cambridge, MA 02140, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 42.84 kDa 
• Atom Count: 2,383 
• Modeled Residue Count: 292 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADAMTS-5	A	378	Homo sapiens	Mutation(s): 0  Gene Names: ADAMTS5, ADAMTS11, ADMP2 EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNA0 (Homo sapiens) Explore Q9UNA0  Go to UniProtKB:  Q9UNA0
PHAROS:  Q9UNA0 GTEx:  ENSG00000154736
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q9UNA0-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BAT	I [auth A]	4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE C23 H31 N3 O4 S2 XFILPEOLDIKJHX-QYZOEREBSA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.260 (Depositor) 
• R-Value Work:  0.230 (Depositor) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.471	α = 90
b = 95.471	β = 90
c = 93.487	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-11 
Deposition Author(s): Mosyak, L., Stahl, M., Somers, W.

Revision History  

• Version 1.0: 2007-12-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary