6HX4 | pdb_00006hx4

Fab fragment of a native monomer-selective antibody in complex with alpha-1-antitrypsin

• PDB DOI: https://doi.org/10.2210/pdb6HX4/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2018-10-15 Released: 2019-10-30 
• Deposition Author(s): Elliston, E.L.K., Miranda, E., Perez, J., Jagger, A.M., Lomas, D.A., Irving, J.A.
• Funding Organization(s): Medical Research Council (United Kingdom), Wellcome Trust, Other private, Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Models: experimental

Literature

Characterisation of a monoclonal antibody conformationally-selective for native alpha-1-antitrypsin

Elliston, E.L.K., Miranda, E., Perez, J., Jagger, A.M., Irving, J.A., Lomas, D.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 185.84 kDa 
• Atom Count: 10,921 
• Modeled Residue Count: 1,522 
• Deposited Residue Count: 1,684 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1-antitrypsin	A, B	397	Homo sapiens	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 1D9 heavy chain	C [auth H], E [auth I]	228	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 1D9 light chain	D [auth L], F [auth M]	217	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 247.48	α = 90
b = 36.75	β = 126.07
c = 201.78	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Elliston, E.L.K., Miranda, E., Perez, J., Jagger, A.M., Lomas, D.A., Irving, J.A.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MR/N024842/1
Wellcome Trust	United Kingdom	Wellcome Trust 4-year PhD Interdisciplinary Programme in Structural, Computational and Chemical Biology
Other private	United States	Alpha-1 Foundation project grant to James Irving
Other private	United States	Alpha-1 Foundation pilot grant to Elena Miranda
Other government	United Kingdom	UCLH/NIHR Biomedical Research Centre

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary