1NL2

BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM AND LYSOPHOSPHOTIDYLSERINE

Structural Biology Knowledgebase: 1NL2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.236

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1NL2

Classification: HYDROLASE

Total Structure Weight: 18375.49

Macromolecule Entities
Molecule Chains Length Organism Details
Prothrombin A 146 Bos taurus EC#: 3.4.21.5 IUBMB
Fragment: FRAGMENT 1 (residues 1-156)
Mutation: E7X, E8X, E15X, E17X, E20X, E21X, E26X, E27X, E30X, E33X
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
LPS
Query on LPS

A O-{HYDROXY[((2R)-2-HYDROXY-3-{[(1S)-1-HYDROXYPENTADECYL]OXY}PROPYL)OXY]PHOSPHORYL}- L-SERINE
LYSOPHOSPHOTIDYLSERINE (Synonym)
C21 H44 N O9 P
RPZLJDFLPRHXGM-HSALFYBXSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CGU
Query on CGU
A L-PEPTIDE LINKING C6 H9 N O6 GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.274
  • R-Value Work: 0.236
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 38.89 α = 90.00
b = 53.22 β = 90.00
c = 128.96 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-01-06
  • Released Date: 2003-09-16
  • Deposition author(s): Huang, M., Huang, G., Furie, B., Seaton, B., Furie, B.C.

Revision History

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