5JFD

Thrombin in complex with (S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1-((benzylsulfonyl)-D-arginyl)pyrrolidine-2-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.163
  • R-Value Work: 0.130

Literature

Macromolecules
Sequence Display for 5JFD

Classification: HYDROLASE

Total Structure Weight: 36532.97

Macromolecule Entities
Molecule Chains Length Organism Details
Prothrombin L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Prothrombin H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Hirudin variant-2 I 12 Hirudo medicinalis Details: http://shop.bachem.com/h-7425.html contains sulfated tyrosine
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
2TS
Query on 2TS

H (2S)-N-[[2-(aminomethyl)-5-chloro-phenyl]methyl]- 1-[(2R)-5-carbamimidamido-2-(phenylmethylsulfonylamino)pentanoyl]pyrrolidine- 2-carboxamide
(S)-1-((R)-5-Guanidino-2-phenylmethanesulfonylamino- pentanoyl)-pyrrolidine-2-carboxylic acid 2aminomethyl- 5-chloro-benzylamide (Synonym)
C26 H36 Cl N7 O4 S
MWLLGEVAEDIFRC-PKTZIBPZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

H N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

H GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

H DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

H SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TYS
Query on TYS
I L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.163
  • R-Value Work: 0.130
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 69.37 α = 90.00
b = 71.49 β = 99.79
c = 72.14 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-04-19
  • Released Date: 2017-05-24
  • Deposition author(s): Sandner, A., Heine, A., Klebe, G.

Revision History

  • Version 1_0: 2017-05-24

    Type: Initial release