3NDD: Cleaved antitrypsin with P10 Pro, and P9-P6 Asp

Cleaved antitrypsin with P10 Pro, and P9-P6 Asp. Determined by X-ray diffraction at 1.5 Å resolution. Released 28 Jul 2010.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,195
Mol. weight: 42.77 kDa
Released: 28 Jul 2010

Explore 3NDD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3NDD contains 15 α-helices and 18 β-strands across 2 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, 15 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
β-strand	111-121	11	2
α-helix	128-138	11
β-strand	140-145	6	2
α-helix	150-164	15
β-strand	182-193	12	2
β-strand	194	1	3
α-helix	197-199	3
α-helix	200-202	3
β-strand	204-211	8	4
β-strand	214-227	14	4
β-strand	228-232	5	1
α-helix	233-235	3
β-strand	237-243	7	1
β-strand	244	1	3
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	4
β-strand	291-298	8	2
α-helix	300-305	6
α-helix	310-312	3
β-strand	327-340	14	2
β-strand	344-357	14	2

Chain B: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
α-helix	360-362	3
β-strand	363-365	3	4
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	343	Homo sapiens	P01009 (AlphaFold model)
Alpha-1-antitrypsin	B	protein	36	Homo sapiens	P01009 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3NDD_1 Alpha-1-antitrypsin (chains A)
GSHMLETFNKITPNLAEFAFSLYRQLAHQSNSTNIFFSPVSIATAFAMLSLGTKADTHDE
ILEGLNFNLTEIPEAQIHEGFQELLRTLNQPDSQLQLTTGNGLFLSEGLKLVDKFLEDVK
KLYHSEAFTVNFGDTEEAKKQINDYVEKGTQGKIVDLVKELDRDTVFALVNYIFFKGKWE
RPFEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHAKKLSSWVLLMKYLGNATAIFFLP
DEGKLQHLENELTHDIITKFLENEDRRSASLHLPKLSITGTYDLKSVLGQLGITKVFSNG
ADLSGVTEEAPLKLSKAVHKAVLTIDEKGTEAAPDDDDEAIPR

Sequence of entity 2 (B), FASTA

>3NDD_2 Alpha-1-antitrypsin (chains B)
SIPPEVKFNKPFVFLMIEQNTKSPLFMGKVVNPTQK

Primary citation

Loop-sheet mechanism of serpin polymerization tested by reactive center loop mutations. Yamasaki, M., Sendall, T.J., Harris, L.E. et al. J Biol Chem (2010) 285:30752-30758. DOI 10.1074/jbc.M110.156042 · 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)
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
6ROD 1.85 Å, Alpha-1-antitrypsin (Ser36Arg/Glu78Arg/Glu266Arg) in the native conformation

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