3BIV

Human thrombin-in complex with UB-THR11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 3BIV

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 35168.15

Macromolecule Entities
Molecule Chains Length Organism Details
Thrombin light chain L 29 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Thrombin heavy chain H 257 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Hirudin I 12 Hirudo medicinalis Fragment: Residues in database 60-71
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
11U
Query on 11U

H (S)-N-(4-carbamimidoylbenzyl)-1-(2-(cyclohexylamino)ethanoyl)pyrrolidine- 2-carboxamide
(2S)-1-[cyclohexylamino)acetyl-N-{4-[amino(imino)methyl]benzyl}pyrrolidine- 2-carboxamide (Synonym)
C21 H31 N5 O2
RYKFVFFOIYLADT-SFHVURJKSA-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
11U Ki: 56100 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind
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: 1.8 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.208
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.70 α = 90.00
b = 71.50 β = 100.90
c = 72.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-12-01
  • Released Date: 2007-12-25
  • Deposition author(s): Gerlach, C., Smolinski, M., Steuber, H., Sotriffer, C.A., Heine, A., Hangauer, D.G., Klebe, G.

Revision History

  • Version 1_0: 2007-12-25

    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: 2013-02-27

    Type: Other