1E04: Plasma beta antithrombin-III

Plasma beta antithrombin-III. Determined by X-ray diffraction at 2.6 Å resolution. Released 2 Jun 2000.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 6,728
Mol. weight: 101.86 kDa
Ligands: PO4, MAN
Released: 2 Jun 2000

Explore 1E04 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1E04 contains 30 α-helices and 38 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, 20 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	16-18	3
α-helix	50-68	19
β-strand	76-78	3	1
α-helix	80-91	12
α-helix	96-105	10
α-helix	108-110	3
α-helix	118-130	13
β-strand	139-149	11	2
β-strand	152-154	3	3
α-helix	156-166	11
β-strand	170-173	4	2
α-helix	175-193	19
α-helix	203	1
β-strand	213-224	12	2
β-strand	225	1	4
α-helix	231-233	3
β-strand	235-240	6	1
β-strand	246-263	18	1
α-helix	264-266	3
β-strand	267-273	7	1
β-strand	274	1	4
β-strand	279-285	7	1
α-helix	292-298	7
α-helix	301-310	10
β-strand	312-321	10	1
β-strand	323-330	8	2
α-helix	332-337	6
α-helix	342-344	3
β-strand	354-356	3	3
β-strand	364-375	12	2
β-strand	379-380	2	2
β-strand	387-390	4	5
β-strand	401-403	3	1
β-strand	408-414	7	1
β-strand	419-426	8	1

Chain L: 14 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	43-68	26
β-strand	76-78	3	5
α-helix	80-91	12
α-helix	96-105	10
α-helix	116-131	16
β-strand	138-149	12	6
β-strand	153-154	2	7
α-helix	156-166	11
β-strand	168-173	6	6
α-helix	175-193	19
α-helix	203	1
β-strand	213-224	12	6
β-strand	225	1	8
α-helix	228-230	3
α-helix	231-233	3
β-strand	235-240	6	5
β-strand	246-262	17	5
β-strand	268-273	6	5
β-strand	274	1	8
β-strand	279-285	7	5
α-helix	292-297	6
α-helix	301-309	9
β-strand	312-322	11	5
β-strand	323-330	8	6
α-helix	332-337	6
α-helix	342-344	3
β-strand	355-357	3	7
β-strand	364-375	12	6
β-strand	379-390	12	6
α-helix	394-396	3
β-strand	408-414	7	5
β-strand	419-426	8	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antithrombin-III	I, L	protein	432	HOMO SAPIENS	P01008 (AlphaFold model)

Sequence of entity 1 (I, L), FASTA

>1E04_1 ANTITHROMBIN-III (chains I, L)
HGSPVDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFAT
TFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIH
FFFAKLNCRLYRKANKSSKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAE
QSRAAINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFY
KADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELT
PEVLQEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRD
DLYVSDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVTFKANRPFLVFIREVPLNTI
IFMGRVANPCVK

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1
MAN	alpha-D-mannopyranose	C6 H12 O6	1

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

Primary citation

Structure of Beta-Antithrombin and the Effect of Glycosylation on Antithrombin'S Heparin Affinity and Activity. Mccoy, A.J., Pei, X.Y., Skinner, R. et al. J Mol Biol (2003) 326:823. DOI 10.1016/S0022-2836(02)01382-7 · 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
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
1DZG 2.8 Å, N135Q-S380C-antithrombin-III

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