1G32

THROMBIN INHIBITOR COMPLEX

Structural Biology Knowledgebase: 1G32 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.209

Literature

Macromolecules
Sequence Display for 1G32

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 35792.05

Macromolecule Entities
Molecule Chains Length Organism Details
PROTHROMBIN A 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: LIGHT CHAIN
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTHROMBIN B 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: HEAVY CHAIN
Gene Name(s): F2 Gene View
HIRUDIN IIB C 11 Hirudo medicinalis Fragment: RESIDUES 55-65
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
R11
Query on R11

B 4-{[1-METHYL-5-(2-METHYL-BENZOIMIDAZOL-1- YLMETHYL)-1H-BENZOIMIDAZOL-2-YLMETHYL]-AMINO}- BENZAMIDINE
C25 H25 N7
IRKPNOLLMNHSOU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
R11 Ki: 780 nM (100) BindingDB

Ki: 780 nM  BindingMOAD
Ki: 780 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TYS
Query on TYS
C L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.209
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 69.60 α = 90.00
b = 70.90 β = 100.40
c = 72.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-10-23
  • Released Date: 2001-10-23
  • Deposition author(s): Nar, H.

Revision History

  • 2013-03-13
    Type: Other | Details: Remove PRD info on PRD molecule with WAIT status
  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords