1H8D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.170

Literature

Macromolecules
Sequence Display for 1H8D

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 35371.46

Macromolecule Entities
Molecule Chains Length Organism Details
THROMBIN H 260 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 29 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
PHW
Query on PHW

H N-[(benzyloxy)carbonyl]-beta-phenyl-D-phenylalanyl- N-{(1S,3E)-1-[dihydroxy(diphenoxy)-lambda~5~- phosphanyl]-4-methoxybut-3-en-1-yl}-L-prolinamide
C45 H48 N3 O9 P
RYHYSOICLVLDDN-JBHUJMBHSA-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: 1.4 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.170
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.64 α = 90.00
b = 71.60 β = 100.35
c = 71.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-02-01
  • Released Date: 2001-02-26
  • Deposition author(s): Skordalakes, E., Dodson, G.G., Green, D., Deadman, J.

Revision History

  • Version 1_0: 2001-02-26

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance

  • Version 1_2: 2012-11-30

    Type: Other

  • Version 1_3: 2013-03-13

    Type: Other

  • Version 1_4: 2017-07-12

    Type: Advisory, Derived calculations