3RLW

Human Thrombin in complex with MI328

Structural Biology Knowledgebase: 3RLW SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.192
  • R-Value Work: 0.163

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3RLW

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 36635.68

Macromolecule Entities
Molecule Chains Length Organism Details
Thrombin Light Chain L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Thrombin Heavy Chain H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Hirudin variant-2 I 13 Hirudo medicinalis Fragment: residues in UNP 60-72
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
S28
Query on S28

H N-(benzylsulfonyl)glycyl-N-(4-carbamimidoylbenzyl)- L-prolinamide
C22 H27 N5 O4 S
CEBNOQRCTYYHRQ-IBGZPJMESA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

H N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

H PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

H SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
S28 Ki: 3.7 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_001087 (PMS,00S,PRO,GLY) H N-(BENZYLSULFONYL)GLYCYL-N-(4-CARBAMIMIDOYLBENZYL)-L-PROLINAMIDE Peptide-like /
Thrombin inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (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: 1.69 Å
  • R-Value Free: 0.192
  • R-Value Work: 0.163
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.50 α = 90.00
b = 71.30 β = 100.60
c = 72.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-04-20
  • Released Date: 2012-04-25
  • Deposition author(s): Biela, A., Heine, A., Klebe, G.

Revision History

  • 2016-07-13
    Type: Citation | Details: Citation update
  • 2012-12-12
    Type: Other | Details: Add PRD info