1P8V

CRYSTAL STRUCTURE OF THE COMPLEX OF PLATELET RECEPTOR GPIB-ALPHA AND ALPHA-THROMBIN AT 2.6A

Structural Biology Knowledgebase: 1P8V SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.207

Literature

Macromolecules
Sequence Display for 1P8V

Classification: MEMBRANE PROTEIN / HYDROLASE

Total Structure Weight: 65037.82

Macromolecule Entities
Molecule Chains Length Organism Details
Platelet glycoprotein Ib alpha chain A 279 Homo sapiens Fragment: Glycoprotein 1B alpha
Mutation: N21D, Y276X
Gene Name(s): GP1BA Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Prothrombin B 29 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: Alpha Thrombin, light chain
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Prothrombin C 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: Alpha Thrombin, heavy chain
Gene Name(s): F2 Gene View

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

C N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MES
Query on MES

A 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DFP
Query on DFP

C DIISOPROPYL PHOSPHONATE
C6 H15 O3 P
BLKXLEPPVDUHBY-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
A L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.207
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 47.10 α = 90.00
b = 111.77 β = 90.00
c = 176.25 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-07
  • Released Date: 2003-07-22
  • Deposition author(s): Dumas, J.J., Kumar, R., Seehra, J., Somers, W.S., Mosyak, L.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update