2ZNH: Domain-Swapped Serpin Dimer

Crystal Structure of a Domain-Swapped Serpin Dimer. Determined by X-ray diffraction at 2.8 Å resolution. Released 21 Oct 2008.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,599
Mol. weight: 100.63 kDa
Ligands: NAG, CIT
Released: 21 Oct 2008

Explore 2ZNH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ZNH contains 29 α-helices and 42 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: 15 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	1
α-helix	46-68	23
β-strand	76-78	3	2
α-helix	80-90	11
α-helix	91-93	3
α-helix	96-105	10
α-helix	108-110	3
β-strand	115	1	1
α-helix	118-130	13
β-strand	139-149	11	3
β-strand	154	1	4
α-helix	156-166	11
β-strand	169-173	5	3
α-helix	175-193	19
β-strand	211-224	14	3
β-strand	225	1	5
α-helix	231-233	3
β-strand	235-240	6	2
β-strand	246-262	17	2
α-helix	264-266	3
β-strand	268-273	6	2
β-strand	274	1	5
β-strand	279-285	7	2
α-helix	292-298	7
α-helix	301-308	8
α-helix	311	1
β-strand	312-321	10	2
β-strand	323-330	8	3
α-helix	331-336	6
α-helix	342-344	3
β-strand	355	1	6
β-strand	363-375	13	7
β-strand	379-391	13	7
β-strand	405	1	2
β-strand	408-414	7	2
β-strand	419-426	8	2

Chain B: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	24-25	2	8
α-helix	46-68	23
β-strand	76-78	3	9
α-helix	80-91	12
α-helix	96-105	10
α-helix	108-110	3
β-strand	114-115	2	8
α-helix	117-130	14
β-strand	139-149	11	7
β-strand	154	1	6
α-helix	156-166	11
β-strand	169-173	5	7
α-helix	175-193	19
β-strand	211-224	14	7
β-strand	225	1	10
α-helix	231-233	3
β-strand	235-240	6	9
β-strand	246-262	17	9
α-helix	264-266	3
β-strand	268-273	6	9
β-strand	274	1	10
β-strand	279-285	7	9
α-helix	292-298	7
α-helix	301-309	9
β-strand	312-321	10	9
β-strand	323-330	8	7
α-helix	331-335	5
α-helix	342-344	3
β-strand	355	1	4
β-strand	362-375	14	3
β-strand	379-392	14	3
α-helix	396-398	3
β-strand	405	1	9
β-strand	408-414	7	9
β-strand	419-426	8	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antithrombin-III	A, B	protein	432	Homo sapiens	P01008 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2ZNH_1 Antithrombin-III (chains A, B)
HGSPVDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFAT
TFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIH
FFFAKLNCRLYRKANKSSKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAE
QSRAAINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFY
KADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELT
PEVLQEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRD
DLYVSDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVTFKANRPFLVFIREVPLNTI
IFMGRVANPCVK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
CIT	Citric acid	C6 H8 O7	2

Primary citation

Crystal structure of a stable dimer reveals the molecular basis of serpin polymerization. Yamasaki, M., Li, W., Johnson, D.J. et al. Nature (2008) 455:1255-1258. DOI 10.1038/nature07394 · PubMed

Other PDB entries of the same protein (UniProt P01008 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KCG 1.7 Å, Crystal structure of the antithrombin-factor IXa-pentasaccharide complex
2B5T 2.1 Å, 2.1 Angstrom structure of a nonproductive complex between antithrombin, synthetic…
1TB6 2.5 Å, 2.5A Crystal Structure of the Antithrombin-Thrombin-Heparin Ternary Complex
1E04 2.6 Å, Plasma beta antithrombin-III
1JVQ 2.6 Å, Crystal structure at 2.6A of the ternary complex between antithrombin, a P14-P8 reactive…
1NQ9 2.6 Å, Crystal Structure of Antithrombin in the Pentasaccharide-Bound Intermediate State
2ANT 2.6 Å, The 2.6 a structure of antithrombin indicates a conformational change at the heparin…
1E05 2.62 Å, Plasma alpha antithrombin-III
1OYH 2.62 Å, Crystal Structure of P13 Alanine Variant of Antithrombin
1R1L 2.7 Å, Structure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide and an…
2BEH 2.7 Å, Crystal structure of antithrombin variant S137A/V317C/T401C with plasma latent…
1T1F 2.75 Å, Crystal Structure of Native Antithrombin in its Monomeric Form

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