5NBV | pdb_00005nbv

Crystal structure of native alpha-1-antitrypsin with seven stabilising mutations

• PDB DOI: https://doi.org/10.2210/pdb5NBV/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-03-02 Released: 2018-03-21 
• Deposition Author(s): Huntington, J.A., Pomowski, A., Johnson, D.J.D.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF THE Z VARIANT OF ALPHA-1-ANTITRYPSIN REVEALS STRUCTURAL AND DYNAMICAL CHANGES AND SUPPORTS A C-TERMINAL DOMAIN SWAP MECHANISM OF POLYMERIZATION

Johnson, D.J.D., Pomowski, A., Huntington, J.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.62 kDa 
• Atom Count: 3,184 
• Modeled Residue Count: 369 
• Deposited Residue Count: 377 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1-antitrypsin	A	377	Homo sapiens	Mutation(s): 9  Gene Names: SERPINA1, AAT, PI, PRO0684, PRO2209
UniProt & NIH Common Fund Data Resources
Find proteins for P01009 (Homo sapiens) Explore P01009  Go to UniProtKB:  P01009
PHAROS:  P01009 GTEx:  ENSG00000197249

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.7	α = 90
b = 39.26	β = 104.08
c = 90.56	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-03-21 
Deposition Author(s): Huntington, J.A., Pomowski, A., Johnson, D.J.D.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MR/L017431/1

Revision History  

• Version 1.0: 2018-03-21
  Type: Initial release
  
• Version 1.1: 2018-10-24
  Changes: Data collection, Derived calculations
• Version 1.2: 2019-10-16
  Changes: Data collection
• Version 1.3: 2024-01-17
  Changes: Advisory, Data collection, Database references, Refinement description