3OHO | pdb_00003oho

catalytic domain of stromelysin-1 in complex with N-Hydroxy-2-(4-methylphenylsulfonamido)acetamide

• PDB DOI: https://doi.org/10.2210/pdb3OHO/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-08-17 Released: 2011-06-29 
• Deposition Author(s): Kowatz, T., Naismith, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.264 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.255 (Depositor) 
• R-Value Observed: 
  0.255 (Depositor) 

Starting Model: experimental

Literature

Non-Resonance Raman Difference Spectroscopy as a Tool to Probe Enthalpy-Entropy Compensation and the Interfacial Mobility Model

Kowatz, T., Naismith, J.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.61 kDa 
• Atom Count: 1,313 
• Modeled Residue Count: 159 
• Deposited Residue Count: 169 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stromelysin-1	A	169	Homo sapiens	Mutation(s): 0  Gene Names: MMP3, STMY1 EC: 3.4.24.17
UniProt & NIH Common Fund Data Resources
Find proteins for P08254 (Homo sapiens) Explore P08254  Go to UniProtKB:  P08254
PHAROS:  P08254 GTEx:  ENSG00000149968

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Z79	G [auth A]	N-hydroxy-N~2~-[(4-methoxyphenyl)sulfonyl]glycinamide C9 H12 N2 O5 S WLZISXXOYYGJNT-UHFFFAOYSA-N
SO4	H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Z79	BindingDB:  3OHO	Ki: 4400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.264 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.255 (Depositor) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.482	α = 90
b = 121.044	β = 90
c = 46.872	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-29 
Deposition Author(s): Kowatz, T., Naismith, J.H.

Revision History  

• Version 1.0: 2011-06-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description