1R1L: Dimeric antithrombin

Structure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide and an exogenous tripeptide (formyl-norleucine-LF). Determined by X-ray diffraction at 2.7 Å resolution. Released 5 Oct 2004.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,898
Mol. weight: 100.82 kDa
Ligands: NAG, FOR
Released: 5 Oct 2004

Explore 1R1L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1R1L contains 33 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	3-6	4	7

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	11	1	7

Chain I: 16 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	12-14	3
β-strand	24	1	5
α-helix	25-27	3
α-helix	46-68	23
β-strand	76-78	3	6
α-helix	80-91	12
α-helix	96-105	10
α-helix	108-110	3
β-strand	115	1	5
α-helix	118-130	13
β-strand	139-149	11	7
β-strand	154	1	8
α-helix	156-166	11
β-strand	169-173	5	7
α-helix	179-193	15
β-strand	213-222	10	7
β-strand	225	1	9
α-helix	231-233	3
β-strand	235-240	6	6
β-strand	246-262	17	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	292-298	7
α-helix	301-309	9
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	1	8
β-strand	366	1	7
β-strand	368-375	8	7
β-strand	386-390	5	1
β-strand	400-403	4	6
β-strand	408-414	7	6
β-strand	419-426	8	6

Chain L: 17 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	44-68	25
β-strand	76-78	3	1
α-helix	80-91	12
α-helix	96-105	10
α-helix	108-110	3
α-helix	119-131	13
β-strand	139-142	4	2
β-strand	145-149	5	2
β-strand	153-154	2	3
α-helix	156-166	11
β-strand	169-173	5	2
α-helix	179-193	15
α-helix	204-206	3
β-strand	213-224	12	2
β-strand	225	1	4
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	4
β-strand	279-285	7	1
α-helix	286-287	2
α-helix	293-296	4
α-helix	301-310	10
β-strand	312-322	11	1
β-strand	323-330	8	2
α-helix	332-338	7
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)
Antithrombin P14-P9 peptide	C	protein	7
EXOGENOUS TRIPEPTIDE formyl-(NLE)LF	D	protein	3

Sequence of entity 1 (I, L), FASTA

>1R1L_1 Antithrombin-III (chains I, L)
HGSPVDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFAT
TFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIH
FFFAKLNCRLYRKANKSSKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAE
QSRAAINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFY
KADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELT
PEVLQEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRD
DLYVSDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVTFKANRPFLVFIREVPLNTI
IFMGRVANPCVK

Sequence of entity 2 (C), FASTA

>1R1L_2 Antithrombin P14-P9 peptide (chains C)
XSEAAAS

Sequence of entity 3 (D), FASTA

>1R1L_3 EXOGENOUS TRIPEPTIDE formyl-(NLE)LF (chains D)
LLF

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7
FOR	Formyl group	C H2 O	1

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

Primary citation

Serpins and the design of peptides to block intermolecular beta-linkages. Zhou, A., Huntington, J.A., Lomas, D.A. 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
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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