1NQ9: Antithrombin-III

Crystal Structure of Antithrombin in the Pentasaccharide-Bound Intermediate State. Determined by X-ray diffraction at 2.6 Å resolution. Released 30 Sept 2003.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,779
Mol. weight: 103.24 kDa
Ligands: NAG
Released: 30 Sept 2003

Explore 1NQ9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NQ9 contains 32 α-helices and 36 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, 18 β-strands

Element	Residues	Length	Sheet
α-helix	46-68	23
β-strand	76-78	3	1
α-helix	80-86	7
α-helix	88-91	4
α-helix	97-105	9
α-helix	113-117	5
α-helix	119-130	12
β-strand	139-149	11	2
α-helix	156-165	10
α-helix	169-170	2
β-strand	171-173	3	2
α-helix	175-193	19
β-strand	213-224	12	2
β-strand	225	1	3
α-helix	228-230	3
α-helix	231-233	3
β-strand	235-240	6	1
β-strand	246-262	17	1
α-helix	264-266	3
β-strand	268-273	6	1
β-strand	274	1	3
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	331-337	7
α-helix	342-344	3
β-strand	366-375	10	2
β-strand	379-380	2	2
β-strand	387-390	4	4
β-strand	400-403	4	1
β-strand	408-414	7	1
β-strand	419-426	8	1

Chain L: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	40-41	2
α-helix	46-67	22
β-strand	76-78	3	4
α-helix	80-91	12
α-helix	96-105	10
α-helix	113-117	5
α-helix	119-131	13
β-strand	139-149	11	5
β-strand	153-154	2	6
α-helix	156-166	11
β-strand	169-173	5	5
α-helix	175-193	19
α-helix	203	1
β-strand	213-224	12	5
β-strand	225	1	7
α-helix	228-230	3
β-strand	235-240	6	4
β-strand	246-262	17	4
α-helix	264-266	3
β-strand	268-273	6	4
β-strand	274	1	7
β-strand	279-285	7	4
α-helix	293-298	6
α-helix	301-310	10
β-strand	312-321	10	4
β-strand	323-330	8	5
α-helix	332-337	6
α-helix	342-344	3
β-strand	355-357	3	6
β-strand	364-375	12	5
β-strand	379-390	12	5
α-helix	395-397	3
β-strand	408-414	7	4
β-strand	419-426	8	4

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

>1NQ9_1 Antithrombin-III (chains I, 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

Primary citation

Crystal Structure of Antithrombin in a Heparin-Bound Intermediate State. Johnson, D.J.D., Huntington, J.A. Biochemistry (2003) 42:8712-8719. DOI 10.1021/bi034524y · 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…
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

Browse structure collections

About this viewer

MolViewer shows 1NQ9 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.