Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6734.48 
• Atom Count: 478 
• Residue Count: 58 
• Unique protein chains: 1

2KNT

THE 1.2 ANGSTROM STRUCTURE OF KUNITZ TYPE DOMAIN C5

• DOI: 10.2210/pdb2KNT/pdb

• Classification: KUNITZ INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae


• 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: 1.2 Å
• R-Value Free: 0.206 

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.,Sect.D 54: 306-312

• PubMed: 9761897 


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
COLLAGEN	A	58	Homo sapiens	Mutation(s): 0  Gene Names: COL6A3
Find proteins for P12111 (Homo sapiens) Go to Gene View: COL6A3 Go to UniProtKB:  P12111

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.2 Å
• R-Value Free: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 25.690	α = 90.00
b = 38.040	β = 109.20
c = 28.640	γ = 90.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance