1B5G

HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC INHIBITOR AND HIRUGEN

Structural Biology Knowledgebase: 1B5G SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Work: 0.164

Literature

Macromolecules
Sequence Display for 1B5G

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 36022.26

Macromolecule Entities
Molecule Chains Length Organism Details
ALPHA-THROMBIN L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ALPHA-THROMBIN 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
0ZE
Query on 0ZE

H [[[(4S,5S)-4-[[(3S,6S,8aR)-6-azanyl-5-oxo- 6-(phenylmethyl)-1,2,3,7,8,8a-hexahydroindolizin- 3-yl]carbonylamino]-5-(1,3-benzothiazol-2- yl)-5-hydroxy-pentyl]amino]-azanyl-methylidene]azanium
MOL-168 (Synonym)
C29 H38 N7 O3 S
DKILHAQNHIMEGI-ICSWELKVSA-O
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: 2.07 Å
  • R-Value Observed:
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.84 α = 90.00
b = 72.08 β = 100.90
c = 73.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-03-05
  • Released Date: 1998-05-27
  • Deposition author(s): St Charles, R., Tulinsky, A., Kahn, M.

Revision History

  • 2015-03-25
    Type: Sequence database correspondence | Details: Correct residue numbering in struct_ref_seq
  • 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
  • 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