6IAY | pdb_00006iay

Alpha-1-antitrypsin Queen's (Lys154Asn) variant

PDB DOI: https://doi.org/10.2210/pdb6IAY/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2018-11-28 Released: 2019-12-18
Deposition Author(s): Aldobiyan, I., Lomas, D.A., Irving, J.A.
Funding Organization(s): Medical Research Council (United Kingdom), Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.241 (Depositor), 0.240 (DCC)
R-Value Work:
0.212 (Depositor), 0.210 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural determinants of instability in alpha-1-antitrypsin

Aldobiyan, I., Irving, J.A., Lomas, D.A.

To be published.

Macromolecule Content

Total Structure Weight: 45.66 kDa
Atom Count: 3,034
Modeled Residue Count: 368
Deposited Residue Count: 404
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1-antitrypsin	A	404	Homo sapiens	Mutation(s): 2 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01009
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLY Query on GLY Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.241 (Depositor), 0.240 (DCC)
R-Value Work: 0.212 (Depositor), 0.210 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.265	α = 90
b = 38.763	β = 104.13
c = 89.712	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-12-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MR/N024842/1
Other government	United Kingdom	UCLH/NIHR Biomedical Research Centre

Revision History (Full details and data files)

Version 1.0: 2019-12-18
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.