1A5G

HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC INHIBITOR AND HIRUGEN

Structural Biology Knowledgebase: 1A5G SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Work: 0.158

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1A5G

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 36036.25

Macromolecule Entities
Molecule Chains Length Organism Details
ALPHA-THROMBIN (SMALL SUBUNIT) L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ALPHA-THROMBIN (LARGE SUBUNIT) H 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
HIRUGEN I 12 Hirudo medicinalis Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
00L
Query on 00L

H (1S,7S)-7-amino-7-benzyl-N-[(1S)-4-carbamimidamido- 1-{(1S)-1-hydroxy-2-oxo-2-[(2-phenylethyl)amino]ethyl}butyl]- 8-oxohexahydro-1H-pyrazolo[1,2-a]pyridazine- 1-carboxamide
MOL-126 (Synonym)
C30 H42 N8 O4
BCHJOEWNJFXZEK-DNHJLFCISA-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)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000618 (PEA,00W,00U) H MOL-126 Peptide-like /
Thrombin Inhibitor
Ligand Explorer
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: 2.06 Å
  • R-Value Observed:
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.81 α = 90.00
b = 72.25 β = 100.80
c = 72.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-02-16
  • Released Date: 1998-05-27
  • Deposition author(s): St Charles, R., Tulinsky, A., Kahn, M.

Revision History

  • 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