3KCG: Antithrombin-factor IXa-pentasaccharide complex

Crystal structure of the antithrombin-factor IXa-pentasaccharide complex. Determined by X-ray diffraction at 1.7 Å resolution. Released 2 Feb 2010.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,669
Mol. weight: 84.99 kDa
Ligands: CA
Released: 2 Feb 2010

Explore 3KCG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KCG contains 30 α-helices and 44 β-strands across 3 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 H: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	3
β-strand	20-21	2	4
α-helix	22-23	2
β-strand	30-34	5	5
β-strand	42-48	7	5
β-strand	51-54	4	5
α-helix	56-58	3
β-strand	65-68	4	5
β-strand	72	1	6
β-strand	81-90	10	5
α-helix	95A-96	3
β-strand	104-108	5	5
β-strand	115	1	7
β-strand	118	1	7
α-helix	120-121	2
β-strand	122	1	4
α-helix	126-131	8
β-strand	135-140	6	4
β-strand	143	1	8
α-helix	150	1
β-strand	151	1	8
α-helix	152	1
β-strand	154	1	6
β-strand	156-163	8	4
α-helix	165-169	5
β-strand	180-183	4	4
β-strand	189	1	3
β-strand	198-203	6	4
β-strand	206-216	11	4
β-strand	226-230	5	4
α-helix	231-234	4
α-helix	235-242	8

Chain I: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	39-41	3
α-helix	46-69	24
β-strand	76-78	3	9
α-helix	80-91	12
α-helix	96-105	10
α-helix	113-117	5
α-helix	119-134	16
β-strand	138-149	12	10
α-helix	156-166	11
α-helix	169-170	2
β-strand	171-173	3	10
α-helix	175-193	19
β-strand	213-223	11	10
β-strand	225	1	11
α-helix	228-230	3
α-helix	231-233	3
β-strand	235-240	6	9
β-strand	246-262	17	9
α-helix	264-266	3
β-strand	268-273	6	9
β-strand	274	1	11
β-strand	279-285	7	9
α-helix	286-287	2
α-helix	292-297	6
α-helix	301-310	10
β-strand	312-321	10	9
β-strand	323-330	8	10
α-helix	332-337	6
α-helix	342-344	3
β-strand	366-375	10	10
β-strand	379	1	11
α-helix	380-385	6
β-strand	391-392	2	4
β-strand	400-403	4	9
β-strand	408-414	7	9
β-strand	419-426	8	9

Chain L: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
α-helix	91-94	4
β-strand	98-101	4	1
β-strand	107-110	4	1
β-strand	115-117	3	2
β-strand	124-126	3	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor IXa light chain	L	protein	59	Homo sapiens	P00740 (AlphaFold model)
Coagulation factor IXa heavy chain	H	protein	235	Homo sapiens	P00740 (AlphaFold model)
Antithrombin-III	I	protein	432	Homo sapiens	P01008 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>3KCG_1 Coagulation factor IXa light chain (chains L)
MDVTCNIKNGRCEQFCKNSADNKVVCSCTEGYRLAENQKSCEPAVPFPCGRVSVSQTSK

Sequence of entity 2 (H), FASTA

>3KCG_2 Coagulation factor IXa heavy chain (chains H)
VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEE
TEHTEQKRNVIRIIPHHNYNAAINKYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFL
KFGSGYVSGWGRVFHKGRSALVLQYLRVPLVDRATCLRSTKFTIYNNMFCAGFHEGGRDS
CQGDAGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT

Sequence of entity 3 (I), FASTA

>3KCG_3 Antithrombin-III (chains I)
HGSPVDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFAT
TFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIH
FFFAKLNCRLYRKANKASKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAE
QSRAAINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFY
KADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELT
PEVLQEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRD
DLYVSDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVTFKANRPFLVFIREVPLNTI
IFMGRVANPCVK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

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

Primary citation

Molecular basis of factor IXa recognition by heparin-activated antithrombin revealed by a 1.7-A structure of the ternary complex. Johnson, D.J., Langdown, J., Huntington, J.A. Proc Natl Acad Sci U S A (2010) 107:645-650. DOI 10.1073/pnas.0910144107 · PubMed

Other PDB entries of the same protein (UniProt P00740 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5JB9 1.3 Å, Crystal structure of factor IXa K98T variant in complex with PPACK
6MV4 1.37 Å, Crystal structure of human coagulation factor ixa
5JBA 1.4 Å, Crystal structure of factor IXa variant V16I K98T Y177T I212V in complex with PPACK
5TNT 1.4 Å, Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa…
4YZU 1.41 Å, Rapid development of two Factor IXa inhibitors from Hit to Lead
4Z0K 1.41 Å, Rapid development of two Factor IXa inhibitors from Hit to Lead
5JB8 1.45 Å, Crystal structure of factor IXa variant K98T in complex with EGR-chloromethylketone
1EDM 1.5 Å, Epidermal growth factor-like domain from human factor IX
2WPH 1.5 Å, factor IXa superactive triple mutant
5TNO 1.54 Å, Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa…
5JBB 1.56 Å, Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with…
2WPJ 1.6 Å, factor IXa superactive triple mutant, NaCl-soaked

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