1UCY

THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A ALPHA (RESIDUES 7-19). THREE COMPLEXES, ONE WITH EPSILON-THROMBIN AND TWO WITH ALPHA-THROMBIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Bovine thrombin complexed with an uncleavable analog of residues 7-19 of fibrinogen A alpha: geometry of the catalytic triad and interactions of the P1', P2', and P3' substrate residues.

Martin, P.D.Malkowski, M.G.DiMaio, J.Konishi, Y.Ni, F.Edwards, B.F.

(1996) Biochemistry 35: 13030-13039

  • DOI: 10.1021/bi960656y

  • PubMed Abstract: 
  • The crystal structure of the noncovalent complex of bovine thrombin and a fibrinogen-A alpha tridecapeptide substrate analog, G17 psi, in which the scissile bond amide nitrogen of Gly-17f has been replaced by a methylene carbon, has been determined a ...

    The crystal structure of the noncovalent complex of bovine thrombin and a fibrinogen-A alpha tridecapeptide substrate analog, G17 psi, in which the scissile bond amide nitrogen of Gly-17f has been replaced by a methylene carbon, has been determined at 2.3 A resolution with an R factor of 17.1%. The geometry of the active site indicates that the crystal structure is a close model of the true Michaelis complex. The three independently determined thrombin/G17 psi complexes in the crystal asymmetric unit reveal novel interactions for the P2' and P3' residues-Pro-18f and Arg-19f, respectively-on the carboxyl-terminal side of the scissile bond and confirm previously observed interactions of the P1 (Arg-16f) through P10 (Asp-7f) positions on the amino-terminal side. The thrombin S2' binding site for Pro-18f, as observed in all three complexes, differs from that predicted by modeling studies and is notable for including two carbonyl oxygens of the thrombin main chain. Arg-19f occupies two binding sites on thrombin, S3'A and S3'B, which have dramatically different placements for the arginyl side chain and carboxyl terminus.


    Organizational Affiliation

    Department of Biochemistry, Wayne State University, Detroit, Michigan 48201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THROMBIN
L, J, M
49Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00735 (Bos taurus)
Go to Gene View: F2
Go to UniProtKB:  P00735
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
THROMBIN
H
150Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00735 (Bos taurus)
Go to Gene View: F2
Go to UniProtKB:  P00735
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
THROMBIN
E
109Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00735 (Bos taurus)
Go to Gene View: F2
Go to UniProtKB:  P00735
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
FIBRINOPEPTIDE A-ALPHA
F, G, I
13Macaca fuscata fuscataMutation(s): 0 
Gene Names: FGA
Find proteins for P68108 (Macaca fuscata fuscata)
Go to Gene View: FGA
Go to UniProtKB:  P68108
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
THROMBIN
K, N
259Bos taurusMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00735 (Bos taurus)
Go to Gene View: F2
Go to UniProtKB:  P00735
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
OPR
Query on OPR
F, G, I
peptide-likeC9 H18 N4 O3

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ACE
Query on ACE
F, G, I
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.470α = 90.00
b = 88.780β = 106.21
c = 98.550γ = 90.00
Software Package:
Software NamePurpose
XENGENdata reduction
XENGENdata scaling
X-PLORrefinement
XENGENdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance