1R1L

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antithrombin-III
L, I
432Homo sapiensGene Names: SERPINC1 (AT3)
Find proteins for P01008 (Homo sapiens)
Go to Gene View: SERPINC1
Go to UniProtKB:  P01008
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antithrombin P14-P9 peptide
C
7N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
EXOGENOUS TRIPEPTIDE formyl-(NLE)LF
D
3N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
I, L
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FOR
Query on FOR

Download SDF File 
Download CCD File 
D
FORMYL GROUP
C H2 O
WSFSSNUMVMOOMR-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NLE
Query on NLE
D
L-PEPTIDE LINKINGC6 H13 N O2LEU
ACE
Query on ACE
C
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.171α = 90.00
b = 100.421β = 104.29
c = 87.198γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
TRUNCATEdata reduction
CCP4data scaling
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-05
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance