Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.28 kDa 
• Atom Count: 2811 
• Residue Count: 338 
• Unique protein chains: 2

1AUT

Human activated protein C

• DOI: 10.2210/pdb1AUT/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1996-06-08 Released: 1997-08-20 
• Deposition Author(s): Mather, T., Oganessyan, V., Hof, P., Bode, W., Huber, R., Foundling, S., Esmon, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work: 0.184 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 3F6U

Literature

The 2.8 A crystal structure of Gla-domainless activated protein C.

Mather, T., Oganessyan, V., Hof, P., Huber, R., Foundling, S., Esmon, C., Bode, W.

(1996) EMBO J 15: 6822-6831

• PubMed: 9003757 
• Primary Citation of Related Structures:  
  1AUT


• PubMed Abstract: 
  

The structure of the Gla-domainless form of the human anticoagulant enzyme activated protein C has been solved at 2.8 A resolution. The light chain is composed of two domains: an epidermal growth factor (EGF)-like domain modified by a large insert containing an additional disulfide, followed by a typical EGF-like domain. The arrangement of the long axis of these domains describes an angle of approximately 80 degrees. Disulfide linked to the light chain is the catalytic domain, which is generally trypsin-like but contains a large insertion loop at the edge of the active site, a third helical segment, a prominent cationic patch analogous to the anion binding exosite I of thrombin and a trypsin-like Ca[II] binding site. The arrangement of loops around the active site partially restricts access to the cleft. The S2 and S4 subsites are much more polar than in factor Xa and thrombin, and the S2 site is unrestricted. While quite open and exposed, the active site contains a prominent groove, the surface of which is very polar with evidence for binding sites on the primed side, in addition to those typical of the trypsin class found on the non-primed side.

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Organizational Affiliation: 

Abteilung Strukturforschung, Max Planck Institut für Biochemie, Martinsried, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTIVATED PROTEIN C	C	250	Homo sapiens	Mutation(s): 0  Gene Names: PROC EC: 3.4.21.69
Find proteins for P04070 (Homo sapiens) Explore P04070  Go to UniProtKB:  P04070
NIH Common Fund Data Resources
PHAROS:  P04070 GTEx:  ENSG00000115718

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTIVATED PROTEIN C	L	114	Homo sapiens	Mutation(s): 0  Gene Names: PROC EC: 3.4.21.69
Find proteins for P04070 (Homo sapiens) Explore P04070  Go to UniProtKB:  P04070
NIH Common Fund Data Resources
PHAROS:  P04070 GTEx:  ENSG00000115718

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0G6	C	D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide C21 H34 Cl N6 O3 DVFLYEYCMMLBTQ-VSZNYVQBSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BHD	L	L-PEPTIDE LINKING	C4 H7 N O5		ASP

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000020 (0G6)	C	D-Phe-Pro-Arg-CH2Cl	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.06	α = 90
b = 89.6	β = 90
c = 101.23	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
MAIN	model building
PROLSQ	refinement
MAIN	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-06-08 
• Released Date: 1997-08-20 
Deposition Author(s): Mather, T., Oganessyan, V., Hof, P., Bode, W., Huber, R., Foundling, S., Esmon, C.

Revision History 

• Version 1.0: 1997-08-20
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-06-20
  Changes: Non-polymer description
• Version 1.4: 2013-02-27
  Changes: Other