5NBU: Alpha-1-antitrypsin

Crystal structure of native alpha-1-antitrypsin with seven stabilising mutations. Determined by X-ray diffraction at 1.67 Å resolution. Released 21 Mar 2018.

Method: X-ray diffraction
Resolution: 1.67 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,296
Mol. weight: 42.7 kDa
Ligands: OXM
Released: 21 Mar 2018

Explore 5NBU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NBU contains 15 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: 15 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	89-104	16
β-strand	112-121	10	2
α-helix	128-138	11
β-strand	141-145	5	2
α-helix	150-164	15
β-strand	182-191	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	256	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	299-305	7
α-helix	310-312	3
β-strand	331-340	10	2
α-helix	348-351	4
α-helix	360-362	3
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	377	Homo sapiens	P01009 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5NBU_1 Alpha-1-antitrypsin (chains A)
GDHPTFNKITPNLAEFAFSLYRQLAHQSNSTNILFSPVSIAAAFAMLSLGAKGDTHDEIL
EGLNFNLTEIPEAQIHEGFQELLRTLNQPDSQLQLTTGNGLFLSEGLKLVDKFLEDVKKL
YHSEAFTVNFGDTEEAKKQINDYVEKGTQGKIVDLVKELDRDTVFALVNYIFFKGKWERP
FEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHSKKLSSWVLLMKYLGNATAIFFLPDE
GKLQHLENELTHDIITKFLENEDRRSASLHLPKLSITGTYDLKSVLGQLGITKVFSNGAD
LSGVTEEAPLKLSKAVHKAVLTIDEKGTEAAGAMFLEAIPMSIPPEVKFNKPFVFLIIEQ
NTKAPLFMGRVVNPTQK

Ligands and cofactors

ID	Name	Formula	Copies
OXM	Oxamic acid	C2 H3 N O3	2

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

Primary citation

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.

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
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
6ROD 1.85 Å, Alpha-1-antitrypsin (Ser36Arg/Glu78Arg/Glu266Arg) in the native conformation

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