1R1L

Structure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide and an exogenous tripeptide (formyl-norleucine-LF)

• PDB DOI: https://doi.org/10.2210/pdb1R1L/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2003-09-24 Released: 2004-10-05 
• Deposition Author(s): Zhou, A., Huntington, J.A., Lomas, D.A., Stein, P.E., Carrell, R.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.204 

Starting Model: experimental

Literature

Serpins and the design of peptides to block intermolecular beta-linkages

Zhou, A., Huntington, J.A., Lomas, D.A., Stein, P.E., Carrell, R.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 100.82 kDa 
• Atom Count: 6,898 
• Modelled Residue Count: 835 
• Deposited Residue Count: 874 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antithrombin-III	A [auth L], B [auth I]	432	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01008 (Homo sapiens) Explore P01008  Go to UniProtKB:  P01008
PHAROS:  P01008 GTEx:  ENSG00000117601

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antithrombin P14-P9 peptide	C	7	N/A	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
EXOGENOUS TRIPEPTIDE formyl-(NLE)LF	D	3	N/A	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth L], F [auth L], G [auth I], H [auth I], I, J [auth I], K [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	L [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FOR	M [auth D]	FORMYL GROUP C H2 O WSFSSNUMVMOOMR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NLE	D	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.204 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.171	α = 90
b = 100.421	β = 104.29
c = 87.198	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
TRUNCATE	data reduction
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-05 
Deposition Author(s): Zhou, A., Huntington, J.A., Lomas, D.A., Stein, P.E., Carrell, R.W.

Revision History  

• Version 1.0: 2004-10-05
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2023-11-15
  Changes: Data collection