1JVQ: Crystal structure

Crystal structure at 2.6A of the ternary complex between antithrombin, a P14-P8 reactive loop peptide, and an exogenous tetrapeptide. Determined by X-ray diffraction at 2.6 Å resolution. Released 3 Jun 2003.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,801
Mol. weight: 101.45 kDa
Ligands: NAG, NDG
Released: 3 Jun 2003

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

Secondary structure: helices and β-sheets

1JVQ contains 28 α-helices and 43 β-strands across 4 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 C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-7	5	8

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	10-11	2	8

Chain I: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
β-strand	24	1	6
α-helix	46-68	23
β-strand	76-78	3	7
α-helix	80-91	12
α-helix	96-105	10
α-helix	108-110	3
β-strand	115	1	6
α-helix	116-130	15
β-strand	139-149	11	8
β-strand	154	1	9
α-helix	156-166	11
β-strand	169-173	5	8
α-helix	179-193	15
β-strand	213-222	10	8
β-strand	225	1	10
α-helix	231-233	3
β-strand	235-240	6	7
β-strand	246-262	17	7
α-helix	264-266	3
β-strand	268-273	6	7
β-strand	274	1	10
β-strand	279-285	7	7
α-helix	292-298	7
α-helix	301-309	9
β-strand	312-321	10	7
β-strand	323-330	8	8
α-helix	332-337	6
α-helix	342-344	3
β-strand	355	1	9
β-strand	366-375	10	8
β-strand	386-390	5	1
β-strand	400-403	4	7
β-strand	408-414	7	7
β-strand	419-426	8	7

Chain L: 14 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	46-67	22
β-strand	76-78	3	1
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	2
β-strand	153-154	2	3
α-helix	156-165	10
β-strand	169-173	5	2
α-helix	175-193	19
α-helix	204-206	3
β-strand	213-224	12	2
β-strand	225	1	4
β-strand	235-236	2	1
β-strand	239-240	2	5
β-strand	246-247	2	5
β-strand	250-262	13	1
α-helix	264-266	3
β-strand	268-273	6	1
β-strand	274	1	4
β-strand	279-285	7	1
α-helix	286-287	2
α-helix	292-296	5
α-helix	301-310	10
β-strand	312-322	11	1
β-strand	323-330	8	2
α-helix	332-337	6
α-helix	342-344	3
β-strand	355-357	3	3
β-strand	364-375	12	2
β-strand	379-390	12	2
β-strand	408-414	7	1
β-strand	419-426	8	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antithrombin-III	I, L	protein	432	Homo sapiens	P01008 (AlphaFold model)
P14-P8 reactive loop peptide	C	protein	8
exogenous Cholecystokinin tetrapeptide	D	protein	5

Sequence of entity 1 (I, L), FASTA

>1JVQ_1 ANTITHROMBIN-III (chains I, L)
HGSPVDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFAT
TFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIH
FFFAKLNCRLYRKANKSSKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAE
QSRAAINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFY
KADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELT
PEVLQEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRD
DLYVSDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVTFKANRPFLVFIREVPLNTI
IFMGRVANPCVK

Sequence of entity 2 (C), FASTA

>1JVQ_2 P14-P8 reactive loop peptide (chains C)
XSEAAAST

Sequence of entity 3 (D), FASTA

>1JVQ_3 exogenous Cholecystokinin tetrapeptide (chains D)
WMDFX

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
NDG	2-acetamido-2-deoxy-alpha-D-glucopyranose	C8 H15 N O6	7

Primary citation

How small peptides block and reverse serpin polymerisation. Zhou, A., Stein, P.E., Huntington, J.A. et al. J Mol Biol (2004) 342:931-941. DOI 10.1016/j.jmb.2004.07.078 · 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
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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