9I2H: Activated factor Xa heavy chain

A 3.3 angstrom cryo-EM structure of an engineered high-affinity human prothrombinase complex. Determined by electron microscopy at 3.28 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 3.28 Å
Organism: Homo sapiens
Chains: 4
Atoms: 13,917
Mol. weight: 205.33 kDa
Ligands: CA, CU, 0GJ
Released: 26 Nov 2025

Explore 9I2H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9I2H contains 44 α-helices and 161 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 A: 18 helices, 62 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	12
β-strand	14-15	2	13
β-strand	33-34	2	13
β-strand	40	1	12
β-strand	41	1	14
α-helix	43-45	3
β-strand	48	1	14
α-helix	50-52	3
β-strand	58	1	15
α-helix	60-61	2
β-strand	62-64	3	15
β-strand	69-75	7	12
β-strand	82	1	16
β-strand	85-86	2	15
β-strand	98	1	17
β-strand	114	1	16
β-strand	119-124	6	12
β-strand	140-145	6	15
β-strand	147	1	17
α-helix	152-156	5
β-strand	159-164	6	15
β-strand	184-191	8	18
β-strand	202-206	5	18
β-strand	209-210	2	18
α-helix	215-216	2
β-strand	218-220	3	19
β-strand	224-232	9	18
β-strand	238-242	5	20
β-strand	249	1	18
β-strand	250	1	21
β-strand	253	1	21
β-strand	257-261	5	20
β-strand	264-271	8	18
β-strand	276	1	19
β-strand	281-282	2	20
α-helix	285-289	5
β-strand	297-299	3	19
β-strand	323-324	2	22
β-strand	327-334	8	23
α-helix	345-347	3
α-helix	348-352	5
β-strand	362-369	8	23
β-strand	371	1	24
β-strand	379	1	24
α-helix	391-394	4
β-strand	397	1	25
β-strand	404-405	2	22
β-strand	408-409	2	26
β-strand	418	1	27
β-strand	451-452	2	26
α-helix	461-463	3
β-strand	472-475	4	25
β-strand	478	1	27
α-helix	483-487	5
β-strand	492	1	27
β-strand	495-498	4	25
β-strand	503	1	28
β-strand	509	1	28
β-strand	514-522	9	29
α-helix	525-527	3
α-helix	531-538	8
α-helix	542-544	3
β-strand	559	1	29
β-strand	561	1	30
β-strand	564	1	30
α-helix	566-568	3
α-helix	570-571	2
β-strand	572-573	2	31
β-strand	579-588	10	29
β-strand	596-598	3	31
β-strand	603-604	2	29
β-strand	609-610	2	29
β-strand	612-613	2	31
β-strand	617	1	29
β-strand	620-626	7	29
β-strand	631-637	7	31
α-helix	642-645	4
β-strand	648-653	6	31
α-helix	661-663	3
β-strand	665-668	4	3

Chain B: 13 helices, 65 β-strands

Element	Residues	Length	Sheet
β-strand	1551-1564	14	32
α-helix	1565-1568	4
α-helix	1570-1572	3
β-strand	1586-1594	9	32
β-strand	1595	1	33
β-strand	1603	1	33
β-strand	1620-1621	2	34
β-strand	1626-1632	7	32
β-strand	1633	1	35
β-strand	1640	1	36
β-strand	1648	1	32
α-helix	1667-1669	3
β-strand	1672	1	36
α-helix	1673	1
β-strand	1677	1	35
β-strand	1680-1684	5	32
α-helix	1686-1688	3
β-strand	1697-1702	6	34
α-helix	1708-1711	4
β-strand	1718-1723	6	34
β-strand	1739-1744	6	37
β-strand	1745-1747	3	38
α-helix	1750-1752	3
β-strand	1778-1780	3	38
β-strand	1791-1792	2	39
β-strand	1797-1803	7	37
β-strand	1812-1816	5	40
β-strand	1820-1823	4	37
β-strand	1829-1831	3	37
β-strand	1833-1836	4	40
β-strand	1841-1847	7	37
β-strand	1852-1853	2	39
β-strand	1856-1858	3	40
α-helix	1862-1865	4
β-strand	1869-1870	2	40
β-strand	1873-1874	2	39
β-strand	1882	1	41
α-helix	1892-1894	3
β-strand	1895-1897	3	42
α-helix	1906-1908	3
β-strand	1920-1921	2	43
β-strand	1935-1938	4	42
β-strand	1943	1	44
β-strand	1944-1945	2	45
β-strand	1947	1	41
β-strand	1948	1	46
β-strand	1951	1	47
β-strand	1953-1954	2	48
β-strand	1959-1960	2	48
β-strand	1964-1970	7	42
β-strand	1977-1978	2	42
β-strand	1990-1991	2	42
β-strand	2002	1	46
α-helix	2007	1
β-strand	2008-2009	2	45
β-strand	2012-2019	8	42
β-strand	2025-2026	2	43
β-strand	2027	1	47
β-strand	2031	1	41
β-strand	2034	1	44
β-strand	2041	1	49
α-helix	2051-2053	3
β-strand	2054-2056	3	49
β-strand	2061	1	50
β-strand	2067	1	50
α-helix	2070-2072	3
β-strand	2084	1	51
β-strand	2095-2110	16	49
β-strand	2113-2114	2	52
β-strand	2119-2120	2	52
β-strand	2121-2130	10	49
β-strand	2137-2138	2	49
β-strand	2140	1	53
β-strand	2147	1	53
β-strand	2150-2151	2	49
β-strand	2160-2181	22	49
β-strand	2186	1	51
β-strand	2189-2193	5	49

Chain H: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
β-strand	30-35	6	3
β-strand	40-46	7	3
β-strand	51-54	4	3
α-helix	56-61	6
β-strand	64-68	5	3
β-strand	72	1	4
β-strand	81-83	3	3
β-strand	85-91	7	3
β-strand	104-108	5	3
β-strand	115	1	5
β-strand	118	1	5
β-strand	122	1	2
α-helix	125-130	6
α-helix	131A-132	3
β-strand	135	1	6
β-strand	137-140	4	2
β-strand	143	1	7
β-strand	151	1	7
β-strand	154	1	4
β-strand	156-158	3	2
β-strand	161	1	6
β-strand	162	1	2
α-helix	165-171	7
β-strand	180-185	6	2
β-strand	189	1	1
β-strand	198-203	6	2
β-strand	206-215	10	2
β-strand	224-230	7	2
α-helix	231-234	4
α-helix	235-241	7

Chain L: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-11	2
α-helix	13	1
α-helix	14-18	5
α-helix	24-31	8
α-helix	34-46	13
α-helix	49-51	3
β-strand	60-63	4	8
β-strand	68-71	4	8
β-strand	76	1	9
β-strand	84	1	9
α-helix	92-95	4
β-strand	100	1	10
β-strand	109	1	10
β-strand	115-117	3	11
β-strand	124-126	3	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Activated factor Xa heavy chain	H	protein	254	Homo sapiens	P00742 (AlphaFold model)
Factor X light chain	L	protein	139	Homo sapiens	P00742 (AlphaFold model)
Coagulation factor V heavy chain	A	protein	709	Homo sapiens	P12259 (AlphaFold model)
Coagulation factor V light chain	B	protein	651	Homo sapiens	P12259 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>9I2H_1 Activated factor Xa heavy chain (chains H)
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTE
QEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWANETLM
KQDTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRHSCMLSSDFRITQNMFCAGYDTKQEDA
CQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTRFLKWIKRSMKTRGLPKA
KSHAPEVITSSPLK

Sequence of entity 2 (L), FASTA

>9I2H_2 Factor X light chain (chains L)
ANSFLEEMKKGHLERECMEETCSYEEAREVFEDSDKTNEFWNKYKDGDQCETSPCQNQGK
CKDGLGEYTCTCLEGFEGKNCELFTRKLCRAFNGDCDQFCKRVQSSVVCSCARGYTLADN
GKACIPTGPYPCGKQTLER

Sequence of entity 3 (A), FASTA

>9I2H_3 Coagulation factor V heavy chain (chains A)
AQLRQFYVAAQGISWSYRPEPTNSSLNLSVTSFKKIVYREYEPYFKKEKPQSTISGLLGP
TLYAEVGDIIKVHFKNKADKPLSIHPQGIRYSKLSEGASYLDHTFPAEKMDDAVAPGREY
TYEWSISEDSGPTHDDPPCLTHIYYSHENLIEDFNSGLIGPLLICKKGTLTEGGTQKTFD
KQIVLLFAVFDESKSWSQSSSLMYTVNGYVNGTMPDITVCAHDHISWHLLGMSSGPELFS
IHFNGQVLEQNHHKVSAITLVSATSTTANMTVGPEGKWIISSLTPKHLQAGMQAYIDIKN
CPKKTRNLKKITREQRRHMKRWEYFIAAEEVIWDYAPVIPANMDKKYRSQHLDNFSNQIG
KHYKKVMYTQYEDESFTKHTVNPNMKEDGILGPIIRAQVRDTLKIVFKNMASRPYSIYPH
GVTFSPYEDEVNSSFTSGRNNTMIRAVQPGETYTYKWNILEFDEPTENDAQCLTRPYYSD
VDIMRDIASGLIGLLLICKSRSLDRRGIQRAADIEQQAVFAVFDENKSWYLEDNINKFCE
NPDEVKRDDPKFYESNIMSTINGYVPESITTLGFCFDDTVQWHFCSVGTQNEILTIHFTG
HSFIYGKRHEDTLTLFPMRGESVTVTMDNVGTWMLTSMNSSPRSKKLRLKFRDVKCIPDD
DEDSYEIFEPPESTVMATRKMHDRLEPEDEESDADYDYQNRLAAALGIR

Sequence of entity 4 (B), FASTA

>9I2H_4 Coagulation factor V light chain (chains B)
SNNGNRRNYYIAAEEISWDYSEFVQRETDIEDSDDIPEDTTYKKVVFRKYLDSTFTKRDP
RGEYEEHLGILGPIIRAEVDDVIQVRFKNLASRPYSLHAHGLSYEKSSEGKTYEDDSPEW
FKEDNAVQPNSSYTYVWHATERSGPESPGSACRAWAYYSAVNPEKDIHSGLIGPLLICQK
GILHKDSNMPMDMREFVLLFMTFDEKKSWYYEKKSRSSWRLTSSEMKKSHEFHAINGMIY
SLPGLKMYEQEWVRLHLLNIGGSQDIHVVHFHGQTLLENGNKQHQLGVWPLLPGSFKTLE
MKASKPGWWLLNTEVGENQRAGMQTPFLIMDRDCRMPMGLSTGIISDSQIKASEFLGYWE
PRLARLNNGGSYNAWSVEKLAAEFASKPWIQVDMQKEVIITGIQTQGAKHYLKSCYTTEF
YVAYSSNQINWQIFKGNSTRNVMYFNGNSDASTIKENQFDPPIVARYIRISPTRAYNRPT
LRLELQGCEVNGCSTPLGMENGKIENKQITASSFKKSWWGDYWEPFRARLNAQGRVNAWQ
AKANNNKQWLEIDLLKIKKITAIITQGCKSLSSEMYVKSYTIHYSEQGVEWKPYRLKSSM
VDKIFEGNTNTKGHVKNFFNPPIISRFIRVIPKTWNQSIALRLELFGCDIY

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
CU	Copper (II) ion	Cu	1
0GJ	L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydr…	C14 H28 Cl N6 O5	1

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

Primary citation

A 3.3- angstrom cryo-EM structure of an engineered high-affinity human prothrombinase complex. Ustok, F.I., Faille, A., Huntington, J.A. Blood (2026) 147:573-583. DOI 10.1182/blood.2025031527 · PubMed

Other PDB entries of the same protein (UniProt P00742 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9I24 1.2 Å, Coagulation factor Xa complex with a2-loop peptide
2JKH 1.25 Å, Factor Xa - cation inhibitor complex
2Y5F 1.29 Å, Factor xa - cation inhibitor complex
2Y5G 1.29 Å, Factor xa - cation inhibitor complex
2Y5H 1.33 Å, Factor xa - cation inhibitor complex
3KL6 1.45 Å, Discovery of Tetrahydropyrimidin-2(1H)-one derivative TAK-442: A potent, selective and…
2PR3 1.5 Å, Factor XA inhibitor
6YYX 1.53 Å, Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with…
3FFG 1.54 Å, Factor XA in complex with the inhibitor (R)-6-(2'-((3- HYDROXYPYRROLIDIN-1-YL)METHYL)BIPH…
7YB9 1.54 Å, Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with…
4Y6D 1.55 Å, Factor Xa complex with GTC000101
2VWO 1.6 Å, Aminopyrrolidine Factor Xa inhibitor

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