2BEH: Antithrombin-III

Crystal structure of antithrombin variant S137A/V317C/T401C with plasma latent antithrombin. Determined by X-ray diffraction at 2.7 Å resolution. Released 1 Nov 2005.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,377
Mol. weight: 100.16 kDa
Ligands: NAG
Released: 1 Nov 2005

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

Secondary structure: helices and β-sheets

2BEH contains 30 α-helices and 40 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 I: 16 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
β-strand	24	1	1
α-helix	46-69	24
β-strand	76-78	3	2
α-helix	80-91	12
α-helix	96-105	10
α-helix	108-110	3
β-strand	115	1	1
α-helix	116-127	12
α-helix	128-132	5
β-strand	139-149	11	3
β-strand	154	1	4
α-helix	156-164	9
α-helix	169-170	2
β-strand	171-173	3	3
α-helix	179-193	15
β-strand	213-224	12	3
β-strand	225	1	5
α-helix	228-230	3
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	301-309	9
β-strand	312-321	10	2
β-strand	323-330	8	3
α-helix	331-337	7
β-strand	355	1	4
β-strand	364-375	12	3
β-strand	379-380	2	3
β-strand	387-390	4	6
β-strand	401-403	3	2
β-strand	408-414	7	2
β-strand	419-426	8	2

Chain L: 14 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	45-69	25
β-strand	76-78	3	6
α-helix	80-91	12
α-helix	96-105	10
α-helix	108-110	3
α-helix	116-131	16
β-strand	139-149	11	7
β-strand	153-154	2	8
α-helix	156-165	10
β-strand	169-173	5	7
α-helix	179-193	15
α-helix	203	1
β-strand	213-224	12	7
β-strand	225	1	9
α-helix	231-233	3
β-strand	235-239	5	6
β-strand	247-262	16	6
α-helix	264-266	3
β-strand	268-273	6	6
β-strand	274	1	9
β-strand	279-285	7	6
α-helix	292-297	6
α-helix	301-310	10
β-strand	312-321	10	6
β-strand	323-330	8	7
α-helix	332-337	6
α-helix	342-344	3
β-strand	355-357	3	8
β-strand	364-375	12	7
β-strand	379-390	12	7
β-strand	408-414	7	6
β-strand	419-426	8	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antithrombin-III	I	protein	432	Homo sapiens	P01008 (AlphaFold model)
Antithrombin-III	L	protein	432	Homo sapiens	P01008 (AlphaFold model)

Sequence of entity 1 (I), FASTA

>2BEH_1 Antithrombin-III (chains I)
HGSPVDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFAT
TFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIH
FFFAKLNCRLYRKANKASKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAE
QSRAAINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFY
KADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELT
PEVLQEWLDELEEMMLCVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRD
DLYVSDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVCFKANRPFLVFIREVPLNTI
IFMGRVANPCVK

Sequence of entity 2 (L), FASTA

>2BEH_2 Antithrombin-III (chains L)
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

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

Primary citation

Crystal structure of monomeric native antithrombin reveals a novel reactive center loop conformation. Johnson, D.J., Langdown, J., Li, W. et al. J Biol Chem (2006) 281:35478-35486. DOI 10.1074/jbc.M607204200 · 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…
1T1F 2.75 Å, Crystal Structure of Native Antithrombin in its Monomeric Form
1DZG 2.8 Å, N135Q-S380C-antithrombin-III

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