1NL1

BOVINE PROTHROMBIN FRAGMENT 1 IN COMPLEX WITH CALCIUM ION

• PDB DOI: https://doi.org/10.2210/pdb1NL1/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.253 
• R-Value Work: 0.219 
• R-Value Observed: 0.219 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.9 kDa 
• Atom Count: 1,424 
• Modelled Residue Count: 147 
• Deposited Residue Count: 147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A	147	Bos taurus	Mutation(s): 10  EC: 3.4.21.5
UniProt
Find proteins for P00735 (Bos taurus) Explore P00735  Go to UniProtKB:  P00735

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CGU	A	L-PEPTIDE LINKING	C6 H9 N O6		GLU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.253 
• R-Value Work: 0.219 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.188	α = 90
b = 53.443	β = 90
c = 128.173	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2003-09-16
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-08-16
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2023-11-15
  Changes: Data collection