1H8I

X-ray crystal structure of human alpha-thrombin with a tripeptide phosphonate inhibitor.

Structural Biology Knowledgebase: 1H8I SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.186

Literature

Macromolecules
Sequence Display for 1H8I

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 34398.51

Macromolecule Entities
Molecule Chains Length Organism Details
THROMBIN H 253 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: THROMBIN HEAVY CHAIN
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
HIRUDIN I I 10 Hirudo medicinalis Fragment: RESIDUES 55 TO 64
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
THROMBIN L 27 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: THROMBIN LIGHT CHAIN
Gene Name(s): F2 Gene View

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PHV
Query on PHV

K N-[(benzyloxy)carbonyl]-beta-phenyl-D-phenylalanyl- N-[(1S)-4-methoxy-1-phosphonobutyl]-L-prolinamide
C33 H40 N3 O8 P
RQOYKJRZXWFGEE-TWLDFKIOSA-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: 1.75 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.186
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.39 α = 90.00
b = 71.30 β = 100.87
c = 72.42 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-02-08
  • Released Date: 2001-03-02
  • Deposition author(s): Skordalakes, E., Dodson, G.G., Green, D., Deadman, J.

Revision History

  • 2013-03-13
    Type: Other | Details: Remove PRD info
  • 2012-11-30
    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 PDBx 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