9TLE: Human prothrombinase with prothrombin

Structure of human prothrombinase with prothrombin. Determined by electron microscopy at 3.1 Å resolution. Released 12 Aug 2026.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 5
Atoms: 18,403
Mol. weight: 270.48 kDa
Ligands: CA
Released: 12 Aug 2026

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

Secondary structure: helices and β-sheets

9TLE contains 64 α-helices and 186 β-strands across 5 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: 19 helices, 59 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	9
β-strand	12-15	4	10
α-helix	20-22	3
β-strand	33-36	4	10
β-strand	40	1	9
β-strand	41	1	11
α-helix	43-45	3
β-strand	48	1	11
α-helix	49-52	4
β-strand	58	1	12
β-strand	62-64	3	12
β-strand	69-75	7	9
β-strand	82	1	13
β-strand	85-86	2	12
β-strand	98	1	14
β-strand	114	1	13
β-strand	119-125	7	9
β-strand	140-145	6	12
β-strand	147	1	14
α-helix	152-156	5
β-strand	159-164	6	12
β-strand	170	1	15
β-strand	176	1	15
β-strand	181	1	16
β-strand	184-191	8	16
β-strand	202-206	5	16
β-strand	209-210	2	16
α-helix	214-216	3
β-strand	218-220	3	17
β-strand	224-232	9	16
β-strand	238-243	6	18
β-strand	249	1	16
β-strand	257-261	5	18
β-strand	264-271	8	16
β-strand	276	1	17
β-strand	280-282	3	18
α-helix	285-290	6
β-strand	297-299	3	17
α-helix	313-317	5
β-strand	323-334	12	19
α-helix	346-350	5
β-strand	362-371	10	19
α-helix	385-388	4
α-helix	393-394	2
β-strand	395-397	3	20
β-strand	404-409	6	19
β-strand	418	1	21
β-strand	451	1	19
β-strand	454-455	2	19
α-helix	461-463	3
β-strand	472-475	4	20
β-strand	478	1	21
α-helix	483-487	5
β-strand	495-498	4	20
β-strand	503	1	22
β-strand	509	1	22
β-strand	514-524	11	23
α-helix	525-527	3
α-helix	531-535	5
α-helix	550-553	4
β-strand	557-559	3	23
β-strand	561	1	24
β-strand	564	1	24
α-helix	566-568	3
α-helix	570-571	2
β-strand	572-575	4	25
β-strand	580-588	9	23
β-strand	596-598	3	25
β-strand	603-604	2	23
β-strand	609-610	2	23
β-strand	612-613	2	25
β-strand	617	1	23
β-strand	620-625	6	23
β-strand	631-637	7	25
α-helix	642-645	4
β-strand	648-654	7	25
β-strand	665-668	4	3
α-helix	690-705	16

Chain B: 10 helices, 63 β-strands

Element	Residues	Length	Sheet
β-strand	1551-1564	14	26
α-helix	1575-1579	5
β-strand	1586-1594	9	26
β-strand	1595	1	27
β-strand	1603	1	27
β-strand	1620-1623	4	28
β-strand	1627-1633	7	26
β-strand	1640	1	29
β-strand	1643	1	30
β-strand	1648	1	26
β-strand	1656	1	31
α-helix	1667-1669	3
β-strand	1672	1	29
β-strand	1677	1	26
β-strand	1680-1683	4	26
α-helix	1686-1688	3
β-strand	1697-1702	6	28
β-strand	1703	1	30
β-strand	1705	1	31
α-helix	1708-1711	4
β-strand	1718-1723	6	28
β-strand	1729	1	32
β-strand	1734	1	32
β-strand	1739-1744	6	33
β-strand	1745-1747	3	34
β-strand	1778-1780	3	34
β-strand	1783	1	34
β-strand	1791-1792	2	35
β-strand	1797-1803	7	33
β-strand	1812-1816	5	35
β-strand	1821-1823	3	33
β-strand	1829-1831	3	33
β-strand	1833-1836	4	35
β-strand	1842-1847	6	33
β-strand	1852-1858	7	35
α-helix	1861-1866	6
β-strand	1869-1874	6	35
α-helix	1875-1876	2
β-strand	1882	1	36
α-helix	1892-1894	3
β-strand	1895-1897	3	37
α-helix	1906-1908	3
β-strand	1920-1921	2	38
β-strand	1935-1937	3	37
β-strand	1943-1945	3	39
β-strand	1947-1951	5	36
β-strand	1953-1955	3	40
β-strand	1958-1960	3	40
β-strand	1964-1970	7	37
β-strand	1976-1978	3	37
β-strand	1990-1991	2	37
β-strand	2000-2001	2	36
β-strand	2008-2010	3	39
β-strand	2012-2019	8	37
β-strand	2025-2026	2	38
β-strand	2027-2031	5	36
β-strand	2034	1	39
β-strand	2041	1	41
α-helix	2051-2053	3
β-strand	2054-2056	3	41
β-strand	2061	1	42
β-strand	2067	1	42
α-helix	2070-2072	3
β-strand	2084	1	43
β-strand	2095-2111	17	41
β-strand	2113-2114	2	44
β-strand	2119-2120	2	44
β-strand	2122-2130	9	41
β-strand	2138	1	41
β-strand	2150-2151	2	41
β-strand	2160-2180	21	41
β-strand	2186	1	43
β-strand	2187-2194	8	41

Chain H: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
β-strand	30-34	5	3
β-strand	40-46	7	3
β-strand	51-54	4	3
β-strand	65-68	4	3
β-strand	72	1	4
β-strand	81-83	3	3
β-strand	85-91	7	3
β-strand	104-108	5	3
α-helix	111-112	2
β-strand	115	1	5
β-strand	118	1	5
β-strand	122	1	2
α-helix	125-127	3
α-helix	128-131A	5
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
α-helix	160	1
β-strand	161	1	6
β-strand	162	1	2
α-helix	165-169	5
β-strand	180-183	4	2
β-strand	189	1	1
β-strand	198-202	5	2
β-strand	207-212	6	2
β-strand	226-230	5	2
α-helix	231-233	3
α-helix	235-241	7

Chain L: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
α-helix	92-95	4
β-strand	115-117	3	8
β-strand	124-126	3	8

Chain P: 27 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	14-18	5
α-helix	24-31	8
α-helix	34-47	14
α-helix	48-50	3
α-helix	55-62	8
β-strand	66	1	45
β-strand	79	1	46
α-helix	84	1
β-strand	85	1	46
β-strand	86	1	47
α-helix	87-88	2
α-helix	105-107	3
β-strand	115	1	48
β-strand	125-127	3	48
β-strand	128	1	47
β-strand	135-137	3	48
β-strand	141	1	49
β-strand	142	1	45
β-strand	148	1	49
α-helix	170	1
β-strand	171	1	50
α-helix	172-174	3
β-strand	184	1	51
α-helix	189	1
β-strand	190	1	51
α-helix	191-193	3
α-helix	197-202	6
β-strand	231	1	52
β-strand	241	1	52
β-strand	247	1	50
α-helix	252-254	3
α-helix	265-270	6
α-helix	277-279	3
α-helix	283-286	4
β-strand	335-340	6	53
β-strand	346-352	7	53
β-strand	357-360	4	53
α-helix	362-364	3
β-strand	366-367	2	54
α-helix	368-370	3
β-strand	372-373	2	54
β-strand	379-383	5	53
β-strand	387	1	55
β-strand	397-406	10	53
β-strand	411	1	56
α-helix	412-415	4
β-strand	417	1	56
β-strand	421-425	5	53
α-helix	428-431	4
β-strand	439	1	57
α-helix	443-451	9
β-strand	455-460	6	57
α-helix	464-467	4
β-strand	479	1	55
β-strand	481-487	7	57
α-helix	490-496	7
β-strand	506-508	3	57
α-helix	519-521	3
β-strand	528-532	5	57
β-strand	539-545	7	57
α-helix	549-551	3
β-strand	558-562	5	57
α-helix	567-575	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Activated factor Xa heavy chain	H	protein	254	Homo sapiens	P00742 (AlphaFold model)
Coagulation factor X	L	protein	110	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)
Prothrombin	P	protein	579	Homo sapiens	P00734 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>9TLE_1 Activated factor Xa heavy chain (chains H)
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTE
QEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWANETLM
KQDTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRHSCMLSSDFRITQNMFCAGYDTKQEDA
CQGDAGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTRFLKWIKRSMKTRGLPKA
KSHAPEVITSSPLK

Sequence of entity 2 (L), FASTA

>9TLE_2 Coagulation factor X (chains L)
MRKLCRAFNGDCDQFCKRVQSSVVCSCARGYTLADNGKACIPTGPYPCGKQTLERRKRSV
AQATSSSGEAPDSITWKPYDAADLDPTENPFDLLDFNQTQPERGDNNLTR

Sequence of entity 3 (A), FASTA

>9TLE_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

>9TLE_4 Coagulation factor V light chain (chains B)
SNNGNRRNYYIAAEEISWDYSEFVQRETDIEDSDDIPEDTTYKKVVFRKYLDSTFTKRDP
RGEYEEHLGILGPIIRAEVDDVIQVRFKNLASRPYSLHAHGLSYEKSSEGKTYEDDSPEW
FKEDNAVQPNSSYTYVWHATERSGPESPGSACRAWAYYSAVNPEKDIHSGLIGPLLICQK
GILHKDSNMPMDMREFVLLFMTFDEKKSWYYEKKSRSSWRLTSSEMKKSHEFHAINGMIY
SLPGLKMYEQEWVRLHLLNIGGSQDIHVVHFHGQTLLENGNKQHQLGVWPLLPGSFKTLE
MKASKPGWWLLNTEVGENQRAGMQTPFLIMDRDCRMPMGLSTGIISDSQIKASEFLGYWE
PRLARLNNGGSYNAWSVEKLAAEFASKPWIQVDMQKEVIITGIQTQGAKHYLKSCYTTEF
YVAYSSNQINWQIFKGNSTRNVMYFNGNSDASTIKENQFDPPIVARYIRISPTRAYNRPT
LRLELQGCEVNGCSTPLGMENGKIENKQITASSFKKSWWGDYWEPFRARLNAQGRVNAWQ
AKANNNKQWLEIDLLKIKKITAIITQGCKSLSSEMYVKSYTIHYSEQGVEWKPYRLKSSM
VDKIFEGNTNTKGHVKNFFNPPIISRFIRVIPKTWNQSIALRLELFGCDIY

Sequence of entity 5 (P), FASTA

>9TLE_5 Prothrombin (chains P)
ANTFLEEVRKGNLERECVEETCSYEEAFEALESSTATDVFWAKYTACETARTPRDKLAAC
LEGNCAEGLGTNYRGHVNITRSGIECQLWRSRYPHKPEINSTTHPGADLQENFCRNPDSS
TTGPWCYTTDPTVRRQECSIPVCGQDQVTVAMTPRSEGSSVNLSPPLEQCVPDRGQQYQG
RLAVTTHGLPCLAWASAQAKALSKHQDFNSAVQLVENFCRNPDGDEEGVWCYVAGKPGDF
GYCDLNYCEEAVEEETGDGLDEDSDRAIEGRTATSEYQTFFNPRTFGSGEADCGLRPLFE
KKSLEDKTERELLESYIDGRIVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLT
AAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDAGGPFVMKSPFNNRWY
QMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

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

Primary citation

Prothrombinase processivity is conferred by substrate allostery. Ustok, F.I., Faille, A., Warren, A.J. et al. EMBO J (2026) 45:3954-3977. DOI 10.1038/s44318-026-00782-4 · 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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