Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.74 kDa 
• Atom Count: 487 
• Modelled Residue Count: 55 
• Deposited Residue Count: 58 
• Unique protein chains: 1

1KNT

THE 1.6 ANGSTROMS STRUCTURE OF THE KUNITZ-TYPE DOMAIN FROM THE ALPHA3 CHAIN OF THE HUMAN TYPE VI COLLAGEN

• PDB DOI: 10.2210/pdb1KNT/pdb

• Classification: COLLAGEN TYPE VI FRAGMENT
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 1994-08-18 Released: 1994-11-01 
• Deposition Author(s): Arnoux, B., Merigeau, K., Saludjian, P., Norris, F., Norris, K., Bjorn, S., Olsen, O., Petersen, L., Ducruix, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Work: 0.189 
• R-Value Observed: 0.189 

Literature

The 1.6 A structure of Kunitz-type domain from the alpha 3 chain of human type VI collagen.

Arnoux, B., Merigeau, K., Saludjian, P., Norris, F., Norris, K., Bjorn, S., Olsen, O., Petersen, L., Ducruix, A.

(1995) J Mol Biol 246: 609-617

• PubMed: 7533217 
• DOI: 10.1016/s0022-2836(05)80110-x
• Primary Citation of Related Structures:  
  1KNT


• PubMed Abstract: 
  

The C-terminal Kunitz-type domain from the alpha 3 chain of human type VI collagen (C5), a single 58 amino acid residue chain with three disulfide bridges, was cloned, expressed and crystallized in a monoclonic form, space group P2(1), with a = 25.7 A, b = 38.2 A, c = 28.8 A and beta = 109 degrees. The structure was resolved by molecular replacement, using Alzheimer's protein precursor inhibitor and bovine pancreatic trypsin inhibitor three-dimensional structures as search models. The molecule with one sulfate ion and 43 associated water molecules was refined by XPLOR to an R-factor of 18.9% at 1.6 A. The molecule was not degraded by trypsin and did not inhibit trypsin or tested serine proteases. As opposed to the other Kunitz family members, C5 demonstrates left-handed chirality of the Cys14-Cys38 disulfide bond. Inversion of the Thr13 carbonyl and bulky side-chains at the interface with trypsin in a model of the C5-trypsin complex may explain the lack of inhibition of trypsin.

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Organizational Affiliation: 

Laboratoire de Biologie Structurale, CNRS, Gif sur Yvette, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COLLAGEN TYPE VI	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
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Work: 0.189 
• R-Value Observed: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.7	α = 90
b = 38.2	β = 109
c = 28.8	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-08-18 
• Released Date: 1994-11-01 
Deposition Author(s): Arnoux, B., Merigeau, K., Saludjian, P., Norris, F., Norris, K., Bjorn, S., Olsen, O., Petersen, L., Ducruix, A.

Revision History  

• Version 1.0: 1994-11-01
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance