9GGP: Alpha-1-antitrypsin

Alpha-1-antitrypsin in complex with the Fab fragment of an anti-polymer antibody. Determined by X-ray diffraction at 1.84 Å resolution. Released 14 May 2025.

Method: X-ray diffraction
Resolution: 1.84 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 6,859
Mol. weight: 138.78 kDa
Released: 14 May 2025

Explore 9GGP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GGP contains 31 α-helices and 60 β-strands across 4 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: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	27-43	17
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	128-137	10
β-strand	141-145	5	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	204-209	6	4
β-strand	215-227	13	4
β-strand	228-232	5	1
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	332-340	9	2
β-strand	344-353	10	2

Chain B: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
α-helix	361-362	2
β-strand	363-365	3	4
β-strand	370-376	7	1
β-strand	382-388	7	1

Chain H: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	5
α-helix	7-9	3
β-strand	10-12	3	6
β-strand	18-25	8	5
β-strand	34-39	6	6
β-strand	45-51	7	6
β-strand	57-59	3	6
α-helix	61-63	3
β-strand	67-72	6	5
α-helix	73-75	3
β-strand	77-82	6	5
α-helix	84-86	3
β-strand	88-97	10	6
β-strand	100C-101	4	6
β-strand	107-111	5	6
α-helix	114-116	3
β-strand	117	1	7
α-helix	118-119	2
β-strand	120-124	5	8
β-strand	134-144	11	8
β-strand	145	1	7
β-strand	150-153	4	9
α-helix	154-156	3
β-strand	162-164	3	8
α-helix	165-167	3
β-strand	168-170	3	8
β-strand	173-183	11	8
β-strand	193-198	6	9
α-helix	199-201	3
β-strand	203-208	6	9

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-13	4	11
β-strand	19-25	7	10
β-strand	33-38	6	11
β-strand	45-49	5	11
β-strand	53-54	2	11
α-helix	55	1
β-strand	62-67	6	10
β-strand	70-75	6	10
α-helix	80-82	3
β-strand	85-90	6	11
β-strand	96-97	2	11
β-strand	101-105	5	11
β-strand	110	1	12
α-helix	111-112	2
β-strand	113-117	5	13
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	13
β-strand	139	1	12
β-strand	144-149	6	14
β-strand	152-154	3	14
β-strand	158-162	5	13
α-helix	163-164	2
α-helix	166	1
β-strand	172-181	10	13
α-helix	182-185	4
β-strand	190-196	7	14
β-strand	204-209	6	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alpha-1-antitrypsin	A, B	protein	404	Homo sapiens	P01009 (AlphaFold model)
Fab fragment heavy chain of 2C1 monoclonal antibody	H	protein	222	Mus musculus
Fab fragment light chain of 2C1 monoclonal antibody	L	protein	212	Mus musculus

Sequence of entity 1 (A, B), FASTA

>9GGP_1 Alpha-1-antitrypsin (chains A, B)
MRGSHHHHHHTDPQGDAAQKTDTSHHDQDHPTFNKITPNLAEFAFSLYRQLAHQSNSTNI
FFSPVSIATAFAMLSLGTKADTHDEILEGLNFNLTEIPEAQIHEGFQELLRTLNQPDSQL
QLTTGNGLFLSEGLKLVDKFLEDVKKLYHSEAFTVNFGDTEEAKKQINDYVEKGTQGKIV
DLVKELDRDTVFALVNYIFFKGKWERPFEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQ
HCKKLSSWVLLMKYLGNATAIFFLPDEGKLQHLENELTHDIITKFLENEDRRSASLHLPK
LSITGTYDLKSVLGQLGITKVFSNGADLSGVTEEAPLKLSKAVHKAVLTIDEKGTEAAGA
MFLEAIPMSIPPEVKFNKPFVFLMIEQNTKSPLFMGKVVNPTQK

Sequence of entity 2 (H), FASTA

>9GGP_2 Fab fragment heavy chain of 2C1 monoclonal antibody (chains H)
DVQLKQSGSSLVQPSQSLSVTCTVSGFSLTSYGVHWVRQSPGKGLEWLGVIWSGGGTDYN
AAFISRLSITKDNSKSQVFFKMNSLQARDTAIYYCARDFYGNYGRYTMNYWGQGTSVTVS
SAKTTPPSVYPLAPGSAAQTNNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQ
SDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR

Sequence of entity 3 (L), FASTA

>9GGP_3 Fab fragment light chain of 2C1 monoclonal antibody (chains L)
DIQVTQTPSSLSASLGGKVTITCKTSQDINKFIAWYQHKPGKGPRLLIHYTSTLQPGIPS
RFSGSGSGRDYSFSISNLEPEDIATYYCLQYDNLYTFGGGTKLEIKRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Primary citation

High-resolution characterization of ex vivo AAT polymers by solution-state NMR spectroscopy. Lowen, S.M., Waudby, C.A., Jagger, A.M. et al. Sci Adv (2025) 11:eadu7064-eadu7064. DOI 10.1126/sciadv.adu7064 · 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
6ROD 1.85 Å, Alpha-1-antitrypsin (Ser36Arg/Glu78Arg/Glu266Arg) in the native conformation

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