Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.73 kDa 
• Atom Count: 528 
• Modelled Residue Count: 58 
• Deposited Residue Count: 58 
• Unique protein chains: 1

2KNT

THE 1.2 ANGSTROM STRUCTURE OF KUNITZ TYPE DOMAIN C5

• PDB DOI: 10.2210/pdb2KNT/pdb

• Classification: KUNITZ INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 1997-01-15 Released: 1997-05-15 
• Deposition Author(s): Merigeau, K., Arnoux, B., Ducruix, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.206 
• R-Value Observed: 0.145 

Literature

1.2 A refinement of the Kunitz-type domain from the alpha3 chain of human type VI collagen.

Merigeau, K., Arnoux, B., Perahia, D., Norris, K., Norris, F., Ducruix, A.

(1998) Acta Crystallogr D Biol Crystallogr 54: 306-312

• PubMed: 9761897 
• DOI: 10.1107/s0907444997010846
• Primary Citation of Related Structures:  
  2KNT


• PubMed Abstract: 
  

The recombinant Kunitz-type domain (C5) of human collagen alpha3(VI) chain was previously described at 1.6 A resolution at room temperature. By changing the crystallization conditions and using synchrotron radiation, we are able to record diffraction data to 1.2 A resolution for crystals of the same space group at 291 K. The protein-water-ion model has been refined anisotropically against these new data using the program SHELXL93; the results converged to an R factor of 15.0%, with all data between 7 and 1.2 A. The final electron-density map reveals a clear chain tracing with a few disordered residues and five residues out of 58 that present alternate conformations. The Cys14-Cys38 bond presents the less frequently observed left-hand conformation (chi1 = -60 degrees). The solvent molecules and a phosphate ion are well ordered with an average B of 38 A2. The high-resolution structure reveals the N and C termini which were missing from the 1.6 A structure.

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Organizational Affiliation: 

Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, 91198 Gif sur Yvette CEDEX, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COLLAGEN	A	58	Homo sapiens	Mutation(s): 0  Gene Names: COL6A3
UniProt & NIH Common Fund Data Resources
Find proteins for P12111 (Homo sapiens) Explore P12111  Go to UniProtKB:  P12111
PHAROS:  P12111

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.206 
• R-Value Observed: 0.145 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.69	α = 90
b = 38.04	β = 109.2
c = 28.64	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
AGROVATA	data reduction
AMoRE	phasing
SHELXL-93	refinement
AGROVATA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-01-15 
• Released Date: 1997-05-15 
Deposition Author(s): Merigeau, K., Arnoux, B., Ducruix, A.

Revision History  

• Version 1.0: 1997-05-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance