7NPK: Alpha-1 antitrypsin C232S

Alpha-1 antitrypsin C232S complexed with CMPD3. Determined by X-ray diffraction at 1.83 Å resolution. Released 7 Apr 2021.

Method: X-ray diffraction
Resolution: 1.83 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,971
Mol. weight: 46.01 kDa
Ligands: UL2
Released: 7 Apr 2021

Explore 7NPK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NPK contains 12 α-helices and 16 β-strands across 1 chain. 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: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	27-44	18
β-strand	50-52	3	1
α-helix	54-65	12
α-helix	70-79	10
α-helix	89-103	15
α-helix	106-109	4
β-strand	112-121	10	2
α-helix	128-138	11
β-strand	141-145	5	2
α-helix	150-164	15
β-strand	182-192	11	2
β-strand	194	1	1
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	256	1
α-helix	260-266	7
α-helix	269-277	9
β-strand	282-289	8	3
β-strand	293-298	6	2
α-helix	299-305	7
α-helix	310-312	3
β-strand	331-340	10	2
β-strand	363-365	3	3
β-strand	370-376	7	1
β-strand	382-388	7	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alpha-1-antitrypsin	A	protein	403	Homo sapiens	P01009 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7NPK_1 Alpha-1-antitrypsin (chains A)
MRGSHHHHHHTDPQGDAAQKTDTSHHDQDHPTFNKITPNLAEFAFSLYRQLAHQSNSTNI
FFSPVSIATAFAMLSLGTKADTHDEILEGLNFNLTEIPEAQIHEGFQELLRTLNQPDSQL
QLTTGNGLFLSEGLKLVDKFLEDVKKLYHSEAFTVNFGDTEEAKKQINDYVEKGTQGKIV
DLVKELDRDTVFALVNYIFFKGKWERPFEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQ
HSKKLSSWVLLMKYLGNATAIFFLPDEGKLQHLENELTHDIITKFLENEDRRSASLHLPK
LSITGTYDLKSVLGQLGITKVFSNGADLSGVTEEAPLKLSKAVHKAVLTIDEKGTEAAGA
MFLEAIPMSIPPEVKFNKPFVFLMIEQNTKSPLFMGKVVNPTQ

Ligands and cofactors

ID	Name	Formula	Copies
UL2	N-((1S,2R)-1-hydroxy-1-(o-tolyl)pentan-2-yl)-2-oxo-2,3-dihydrobenzo[d]oxazole-5…	C20 H22 N2 O4	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

The development of highly potent and selective small molecule correctors of Z alpha 1 -antitrypsin misfolding. Liddle, J., Pearce, A.C., Arico-Muendel, C. et al. Bioorg Med Chem Lett (2021) 41:127973-127973. DOI 10.1016/j.bmcl.2021.127973 · 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
9GGP 1.84 Å, Alpha-1-antitrypsin in complex with the Fab fragment of an anti-polymer antibody
6ROD 1.85 Å, Alpha-1-antitrypsin (Ser36Arg/Glu78Arg/Glu266Arg) in the native conformation

Browse structure collections

About this viewer

MolViewer shows 7NPK directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.