3DT0

Understanding Thrombin Inhibition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Understanding Thrombin Inhibition

Baum, B.Hangauer, D.Heine, A.Klebe, G.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thrombin light chain
L
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Thrombin heavy chain
H
259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Hirudin variant-1
I
11Hirudo medicinalisMutation(s): 0 
Find proteins for P01050 (Hirudo medicinalis)
Go to UniProtKB:  P01050
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
16U
Query on 16U

Download SDF File 
Download CCD File 
H
N-(3-chlorobenzyl)-1-(4-methylpentanoyl)-L-prolinamide
C18 H25 Cl N2 O2
PQUULPKGCNPPBX-INIZCTEOSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000590 (16U)
Query on PRD_000590
HN-(3-chlorobenzyl)-1-(4-methylpentanoyl)-L-prolinamidePeptide-like / Thrombin inhibitor

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Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
I
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.020α = 90.00
b = 71.380β = 100.14
c = 72.290γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SHELXmodel building
MAR345data collection
CNSphasing
SHELXL-97refinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-12-12
    Type: Other
  • Version 1.3: 2016-05-25
    Type: Source and taxonomy
  • Version 1.4: 2017-10-25
    Type: Refinement description