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)

Macromolecule Content

• Total Structure Weight: 48.16 kDa 
• Atom Count: 3300 
• Residue Count: 409 
• Unique protein chains: 1

3K7L

Structures of two elapid snake venom metalloproteases with distinct activities highlight the disulfide patterns in the D domain of ADAMalysin family proteins

• DOI: 10.2210/pdb3K7L/pdb

• Classification: HYDROLASE
• Organism(s): Naja atra
• Mutation(s): No 


• Deposited: 2009-10-13 Released: 2010-03-02 
• Deposition Author(s): Guan, H.H., Wu, W.G., Chen, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.234 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 

Literature

Structures of two elapid snake venom metalloproteases with distinct activities highlight the disulfide patterns in the D domain of ADAMalysin family proteins

Guan, H.H., Goh, K.S., Davamani, F., Wu, P.L., Huang, Y.W., Jeyakanthan, J., Wu, W.G., Chen, C.J.

(2010) J Struct Biol 169: 294-303

• PubMed: 19932752 
• DOI: 10.1016/j.jsb.2009.11.009
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The structures of snake venom metalloproteases (SVMPs) are proposed to be useful models to understand the structural and functional relationship of ADAM (a disintegrin and metalloprotease) which are membrane-anchored proteins involved in multiple human diseases. We have purified, sequenced and determined the structures of two new P-III SVMPs - atragin and kaouthiagin-like (K-like) from Naja atra. Atragin exhibits a known C-shaped topology, whereas K-like adopts an I-shaped conformation because of the distinct disulfide pattern in the disintegrin-like (D) domain. K-like exhibits an enzymatic specificity toward pro-TNFalpha with less inhibition of cell migration, but atragin shows the opposite effect. The specificity of the enzymatic activity is indicated to be dominated mainly by the local structures of SVMP in the metalloprotease (M) domain, whereas the hyper-variable region (HVR) in the cysteine-rich (C) domain is involved in a cell-migration activity. We demonstrate also a pH-dependent enzymatic activity of atragin that we correlate with the structural dynamics of a Zn(2+)-binding motif and the Met-turn based on the structures determined with a pH-jump method. The structural variations between the C- and I-shapes highlight the disulfide bond patterns in the D domain of the ADAM/adamalysin/reprolysins family proteins.

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Organizational Affiliation: 

Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Atragin	A	422	Naja atra	Mutation(s): 0  EC: 3.4.24
Find proteins for D3TTC2 (Naja atra) Explore D3TTC2  Go to UniProtKB:  D3TTC2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.234 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.65	α = 90
b = 91.65	β = 90
c = 124.235	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-13 
• Released Date: 2010-03-02 
Deposition Author(s): Guan, H.H., Wu, W.G., Chen, C.J.

Revision History 

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary