2B4X: Antithrombin-III

Crystal Structure of Antithrombin-III. Determined by X-ray diffraction at 2.8 Å resolution. Released 10 Oct 2006.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,560
Mol. weight: 99.27 kDa
Ligands: NAG
Released: 10 Oct 2006

Explore 2B4X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2B4X contains 24 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 I: 14 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
β-strand	24	1	1
α-helix	25-27	3
α-helix	46-68	23
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	116-130	15
β-strand	139-149	11	3
α-helix	156-164	9
β-strand	172-173	2	3
α-helix	185-193	9
β-strand	213-222	10	3
β-strand	224	1	4
β-strand	225	1	5
α-helix	231-233	3
β-strand	235-239	5	6
β-strand	247-260	14	6
β-strand	262-263	2	2
α-helix	264-266	3
β-strand	267-273	7	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	6
β-strand	323-330	8	3
α-helix	331-337	7
β-strand	366-375	10	3
β-strand	379	1	4
β-strand	387-390	4	7
β-strand	400-403	4	6
β-strand	408-414	7	2
β-strand	419-426	8	2

Chain L: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	45-67	23
β-strand	76-78	3	7
α-helix	80-93	14
α-helix	98-105	8
α-helix	118-131	14
β-strand	139-149	11	8
α-helix	156-165	10
β-strand	169-173	5	8
α-helix	179-193	15
β-strand	214-224	11	8
β-strand	225	1	9
β-strand	235	1	7
β-strand	238-240	3	10
β-strand	246-248	3	10
β-strand	251-260	10	7
β-strand	263	1	11
β-strand	267	1	11
β-strand	268-273	6	7
β-strand	274	1	9
β-strand	279-285	7	7
α-helix	293-296	4
α-helix	303-310	8
β-strand	312-321	10	7
β-strand	323-330	8	8
α-helix	332-337	6
α-helix	342-344	3
β-strand	364-375	12	8
β-strand	379-390	12	8
β-strand	408-414	7	7
β-strand	419-426	8	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antithrombin-III	I	protein	427	Homo sapiens	P01008 (AlphaFold model)
Antithrombin-III	L	protein	427	Homo sapiens	P01008 (AlphaFold model)

Sequence of entity 1 (I), FASTA

>2B4X_1 Antithrombin-III (chains I)
VDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFATTFYQ
HLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIHFFFA
KLNCRLYRKAAKSSKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAEQSRA
AINKWVSNKTEGRITDVIPSEAINELTVLVLVNTILFKGLWKSKFSPENTRKELFYKADG
ESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELTPEVL
QEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRDDLYV
SDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVTFKANRPFLVFIREVPLNTIIFMG
RVANPCV

Sequence of entity 2 (L), FASTA

>2B4X_2 Antithrombin-III (chains L)
VDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFATTFYQ
HLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIHFFFA
KLNCRLYRKANKSSKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAEQSRA
AINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFYKADG
ESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELTPEVL
QEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRDDLYV
SDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVTFKANRPFLVFIREVPLNTIIFMG
RVANPCV

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Crystal Structure of Antithrombin-III. Adams, T.E., Huntington, J.A., Johnson, D.J.D. et al. To be published.

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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