3RMO

Human Thrombin in complex with MI004

Structural Biology Knowledgebase: 3RMO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.165
  • R-Value Work: 0.134

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3RMO

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 36661.17

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
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):

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
S04
Query on S04

H N-(benzylsulfonyl)-3-cyclohexyl-D-alanyl- N-[2-(aminomethyl)-5-chlorobenzyl]-L-prolinamide
C29 H39 Cl N4 O4 S
SMGIPPNIBFQJBW-SXOMAYOGSA-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 %)
S04 Ki: 0.052 - 0.108 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_001005 (PMS,ZAL,PRO,00T) H N-(BENZYLSULFONYL)-3-CYCLOHEXYL-D-ALANYL-N-[2-(AMINOMETHYL)-5-CHLOROBENZYL]-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: 1.4 Å
  • R-Value Free: 0.165
  • R-Value Work: 0.134
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.12 α = 90.00
b = 71.03 β = 100.40
c = 72.75 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-04-21
  • Released Date: 2012-04-25
  • Deposition author(s): Biela, A., Heine, A., Klebe, G.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info