4PYW: Alpha-1-antitrypsin

1.92 angstrom crystal structure of A1AT:TTAI ternary complex. Determined by X-ray diffraction at 1.91 Å resolution. Released 10 Jun 2015.

Method: X-ray diffraction
Resolution: 1.91 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 3,052
Mol. weight: 46.65 kDa
Released: 10 Jun 2015

Explore 4PYW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4PYW contains 14 α-helices and 18 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	27-42	16
β-strand	50-52	3	1
α-helix	54-65	12
α-helix	70-79	10
α-helix	89-103	15
β-strand	111-121	11	2
α-helix	128-138	11
β-strand	141-145	5	2
α-helix	150-164	15
β-strand	182-191	10	2
β-strand	194	1	1
α-helix	197-199	3
α-helix	200-202	3
β-strand	204-211	8	3
β-strand	214-227	14	3
β-strand	228-232	5	1
β-strand	237-244	8	1
β-strand	248-255	8	1
α-helix	260-266	7
α-helix	269-277	9
β-strand	282-289	8	3
β-strand	291-298	8	2
α-helix	299-304	6
α-helix	310-312	3
α-helix	318-320	3
β-strand	333-340	8	2
α-helix	360-362	3
β-strand	363-365	3	3
β-strand	370-376	7	1
β-strand	382-388	7	1

Chains B and C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-4	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alpha-1-antitrypsin	A	protein	404	Homo sapiens	P01009 (AlphaFold model)
Ace-thr-thr-ala-ile-NH2	B, C	protein	6	synthetic construct

Sequence of entity 1 (A), FASTA

>4PYW_1 Alpha-1-antitrypsin (chains A)
MRGSHHHHHHTDPQGDAAQKTDTSHHDQDHPTFNKITPNLAEFAFSLYRQLAHQSNSTNI
FFSPVSIATAFAMLSLGTKADTHDEILEGLNFNLTEIPEAQIHEGFQELLRTLNQPDSQL
QLTTGNGLFLSEGLKLVDKFLEDVKKLYHSEAFTVNFGDTEEAKKQINDYVEKGTQGKIV
DLVKELDRDTVFALVNYIFFKGKWERPFEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQ
HCKKLSSWVLLMKYLGNATAIFFLPDEGKLQHLENELTHDIITKFLENEDRRSASLHLPK
LSITGTYDLKSVLGQLGITKVFSNGADLSGVTEEAPLKLSKAVHKAVLTIDEKGTEAAGA
MFLEAIPMSIPPEVKFNKPFVFLMIEQNTKSPLFMGKVVNPTQK

Sequence of entity 2 (B, C), FASTA

>4PYW_2 ACE-THR-THR-ALA-ILE-NH2 (chains B, C)
XTTAIX

Primary citation

An integrative approach combining ion mobility mass spectrometry, X-ray crystallography, and nuclear magnetic resonance spectroscopy to study the conformational dynamics of alpha 1 -antitrypsin upon ligand binding. Nyon, M.P., Prentice, T., Day, J. et al. Protein Sci (2015) 24:1301-1312. DOI 10.1002/pro.2706 · PubMed

Other PDB entries of the same protein (UniProt P01009 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PI2 1.48 Å, Native alpha-1-antitrypsin at 1.5 Angstrom (Cys232Ser)
3NDD 1.5 Å, Cleaved antitrypsin with P10 Pro, and P9-P6 Asp
6I7U 1.55 Å, Alpha-1-antitrypsin (Ala250Met) in the native conformation
5NBU 1.67 Å, Crystal structure of native alpha-1-antitrypsin with seven stabilising mutations
8QZ5 1.69 Å, Alpha-1-antitrypsin (Tyr244Phe) in the native conformation
5NBV 1.73 Å, Crystal structure of native alpha-1-antitrypsin with seven stabilising mutations
7AEL 1.76 Å, alpha 1-antitrypsin (C232S) complexed with GSK716
6I4V 1.78 Å, Alpha-1-antitrypsin Queen's (K154N) variant
3NE4 1.81 Å, 1.8 Angstrom structure of intact native wild-type alpha-1-antitrypsin
7NPL 1.82 Å, Alpha-1 antitrypsin (C232S) complexed with cmpd 11
7NPK 1.83 Å, Alpha-1 antitrypsin C232S complexed with CMPD3
9GGP 1.84 Å, Alpha-1-antitrypsin in complex with the Fab fragment of an anti-polymer antibody

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