8TN9: Coagulation factor V

Structural architecture of the acidic region of the B domain of coagulation factor V. Determined by electron microscopy at 3.05 Å resolution. Released 4 Oct 2023.

Method: Electron microscopy
Resolution: 3.05 Å
Organism: Homo sapiens
Chains: 1
Atoms: 11,145
Mol. weight: 249.86 kDa
Ligands: NAG
Released: 4 Oct 2023

Explore 8TN9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TN9 contains 27 α-helices and 117 β-strands across 1 chain. 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: 27 helices, 117 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-12	9	1
β-strand	36-40	5	1
β-strand	41	1	2
β-strand	48	1	2
α-helix	49-52	4
β-strand	64-65	2	3
β-strand	69-74	6	1
β-strand	82	1	4
β-strand	85	1	5
β-strand	98	1	6
α-helix	106-108	3
β-strand	114	1	4
α-helix	115	1
β-strand	122-125	4	1
β-strand	139-144	6	3
β-strand	145	1	5
β-strand	147	1	6
α-helix	150-155	6
β-strand	157	1	1
β-strand	160-165	6	3
β-strand	170	1	7
β-strand	176	1	7
β-strand	181-189	9	8
α-helix	192-194	3
β-strand	205-206	2	8
β-strand	209-210	2	8
β-strand	214-219	6	9
β-strand	224	1	10
β-strand	225-233	9	8
β-strand	238-243	6	9
β-strand	248-250	3	11
β-strand	253-255	3	11
β-strand	257-261	5	9
β-strand	264-268	5	8
β-strand	271	1	10
β-strand	276-282	7	9
α-helix	285-289	5
β-strand	294-298	5	9
α-helix	302-304	3
β-strand	323-325	3	12
β-strand	328-330	3	13
β-strand	333	1	14
β-strand	363	1	14
β-strand	366-368	3	13
β-strand	371	1	12
α-helix	392-395	4
β-strand	396-397	2	15
β-strand	402-406	5	12
β-strand	415	1	16
β-strand	418-419	2	17
α-helix	427-429	3
β-strand	447	1	16
α-helix	448	1
β-strand	454-458	5	12
β-strand	472-476	5	15
β-strand	477-478	2	17
α-helix	483-487	5
β-strand	494-498	5	15
β-strand	512-523	12	18
α-helix	525-527	3
α-helix	531	1
α-helix	532-536	5
α-helix	552-555	4
β-strand	558-561	4	18
β-strand	564	1	18
α-helix	566-568	3
α-helix	569-571	3
β-strand	572	1	19
β-strand	575	1	20
β-strand	579-586	8	18
β-strand	594-598	5	19
β-strand	605	1	21
β-strand	608	1	21
β-strand	612-615	4	19
β-strand	617	1	18
β-strand	620-626	7	18
β-strand	631-637	7	19
β-strand	648-653	6	19
β-strand	654	1	20
β-strand	1513	1	22
β-strand	1515	1	22
α-helix	1536-1543	8
β-strand	1551-1562	12	23
β-strand	1588-1595	8	23
β-strand	1603	1	23
β-strand	1620-1623	4	24
β-strand	1627-1634	8	23
β-strand	1640	1	25
β-strand	1643-1644	2	24
β-strand	1648-1649	2	23
β-strand	1672	1	25
β-strand	1676-1683	8	23
α-helix	1686-1688	3
β-strand	1697-1703	7	24
α-helix	1708-1711	4
β-strand	1717-1723	7	24
β-strand	1728	1	26
β-strand	1735	1	26
β-strand	1739-1744	6	27
β-strand	1746-1747	2	28
β-strand	1778-1779	2	28
β-strand	1785	1	29
β-strand	1791-1793	3	29
β-strand	1797-1803	7	27
β-strand	1812-1816	5	29
β-strand	1821-1823	3	27
β-strand	1829-1831	3	27
β-strand	1833-1836	4	29
β-strand	1842-1847	6	27
β-strand	1852-1858	7	29
α-helix	1861-1864	4
β-strand	1869-1875	7	29
β-strand	1881-1882	2	30
α-helix	1892-1894	3
β-strand	1895-1897	3	31
α-helix	1907-1910	4
β-strand	1920-1921	2	32
α-helix	1932-1934	3
β-strand	1935-1937	3	31
β-strand	1943-1950	8	30
β-strand	1951	1	33
β-strand	1955	1	34
β-strand	1958	1	34
β-strand	1961-1970	10	31
β-strand	1977-1978	2	31
β-strand	1990	1	31
β-strand	2000-2010	11	30
β-strand	2012-2021	10	31
β-strand	2025-2026	2	32
β-strand	2027	1	33
β-strand	2030-2034	5	30
β-strand	2041	1	35
β-strand	2055-2056	2	36
β-strand	2061-2062	2	37
β-strand	2066-2067	2	37
β-strand	2095-2110	16	36
β-strand	2122-2130	9	36
β-strand	2137-2138	2	36
α-helix	2139	1
α-helix	2147-2149	3
β-strand	2150-2151	2	36
β-strand	2160-2180	21	36
β-strand	2189-2194	6	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor V	A	protein	2196	Homo sapiens	P12259 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8TN9_1 Coagulation factor V (chains A)
AQLRQFYVAAQGISWSYRPEPTNSSLNLSVTSFKKIVYREYEPYFKKEKPQSTISGLLGP
TLYAEVGDIIKVHFKNKADKPLSIHPQGIRYSKLSEGASYLDHTFPAEKMDDAVAPGREY
TYEWSISEDSGPTHDDPPCLTHIYYSHENLIEDFNSGLIGPLLICKKGTLTEGGTQKTFD
KQIVLLFAVFDESKSWSQSSSLMYTVNGYVNGTMPDITVCAHDHISWHLLGMSSGPELFS
IHFNGQVLEQNHHKVSAITLVSATSTTANMTVGPEGKWIISSLTPKHLQAGMQAYIDIKN
CPKKTRNLKKITREQRRHMKRWEYFIAAEEVIWDYAPVIPANMDKKYRSQHLDNFSNQIG
KHYKKVMYTQYEDESFTKHTVNPNMKEDGILGPIIRAQVRDTLKIVFKNMASRPYSIYPH
GVTFSPYEDEVNSSFTSGRNNTMIRAVQPGETYTYKWNILEFDEPTENDAQCLTRPYYSD
VDIMRDIASGLIGLLLICKSRSLDRRGIQRAADIEQQAVFAVFDENKSWYLEDNINKFCE
NPDEVKRDDPKFYESNIMSTINGYVPESITTLGFCFDDTVQWHFCSVGTQNEILTIHFTG
HSFIYGKRHEDTLTLFPMRGESVTVTMDNVGTWMLTSMNSSPRSKKLRLKFRDVKCIPDD
DEDSYEIFEPPESTVMATRKMHDRLEPEDEESDADYDYQNRLAAALGIRSFRNSSLNQEE
EEFNLTALALENGTEFVSSNTDIIVGSNYSSPSNISKFTVNNLAEPQKAPSHQQATTAGS
PLRHLIGKNSVLNSSTAEHSSPYSEDPIEDPLQPDVTGIRLLSLGAGEFKSQEHAKHKGP
KVERDQAAKHRFSWMKLLAHKVGRHLSQDTGSPSGMRPWEDLPSQDTGSPSRMRPWKDPP
SDLLLLKQSNSSKILVGRWHLASEKGSYEIIQDTDEDTAVNNWLISPQNASRAWGESTPL
ANKPGKQSGHPKFPRVRHKSLQVRQDGGKSRLKKSQFLIKTRKKKKEKHTHHAPLSPRTF
HPLRSEAYNTFSERRLKHSLVLHKSNETSLPTDLNQTLPSMDFGWIASLPDHNQNSSNDT
GQASCPPGLYQTVPPEEHYQTFPIQDPDQMHSTSDPSHRSSSPELSEMLEYDRSHKSFPT
DISQMSPSSEHEVWQTVISPDLSQVTLSPELSQTNLSPDLSHTTLSPELIQRNLSPALGQ
MPISPDLSHTTLSPDLSHTTLSLDLSQTNLSPELSQTNLSPALGQMPLSPDLSHTTLSLD
FSQTNLSPELSHMTLSPELSQTNLSPALGQMPISPDLSHTTLSLDFSQTNLSPELSQTNL
SPALGQMPLSPDPSHTTLSLDLSQTNLSPELSQTNLSPDLSEMPLFADLSQIPLTPDLDQ
MTLSPDLGETDLSPNFGQMSLSPDLSQVTLSPDISDTTLLPDLSQISPPPDLDQIFYPSE
SSQSLLLQEFNESFPYPDLGQMPSPSSPTLNDTFLSKEFNPLVIVGLSKDGTDYIEIIPK
EEVQSSEDDYAEIDYVPYDDPYKTDVRTNINSSRDPDNIAAWYLRSNNGNRRNYYIAAEE
ISWDYSEFVQRETDIEDSDDIPEDTTYKKVVFRKYLDSTFTKRDPRGEYEEHLGILGPII
RAEVDDVIQVRFKNLASRPYSLHAHGLSYEKSSEGKTYEDDSPEWFKEDNAVQPNSSYTY
VWHATERSGPESPGSACRAWAYYSAVNPEKDIHSGLIGPLLICQKGILHKDSNMPMDMRE
FVLLFMTFDEKKSWYYEKKSRSSWRLTSSEMKKSHEFHAINGMIYSLPGLKMYEQEWVRL
HLLNIGGSQDIHVVHFHGQTLLENGNKQHQLGVWPLLPGSFKTLEMKASKPGWWLLNTEV
GENQRAGMQTPFLIMDRDCRMPMGLSTGIISDSQIKASEFLGYWEPRLARLNNGGSYNAW
SVEKLAAEFASKPWIQVDMQKEVIITGIQTQGAKHYLKSCYTTEFYVAYSSNQINWQIFK
GNSTRNVMYFNGNSDASTIKENQFDPPIVARYIRISPTRAYNRPTLRLELQGCEVNGCST
PLGMENGKIENKQITASSFKKSWWGDYWEPFRARLNAQGRVNAWQAKANNNKQWLEIDLL
KIKKITAIITQGCKSLSSEMYVKSYTIHYSEQGVEWKPYRLKSSMVDKIFEGNTNTKGHV
KNFFNPPIISRFIRVIPKTWNQSIALRLELFGCDIY

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Structural architecture of the acidic region of the B domain of coagulation factor V. Mohammed, B.M., Basore, K., Summers, B. et al. J Thromb Haemost (2024) 22:709-714. DOI 10.1016/j.jtha.2023.11.003 · PubMed

Other PDB entries of the same protein (UniProt P12259 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9I24 1.2 Å, Coagulation factor Xa complex with a2-loop peptide
3P6Z 1.7 Å, Structural basis of thrombin mediated factor V activation: essential role of the…
3S9C 1.8 Å, Russell's viper venom serine proteinase, RVV-V in complex with the fragment (residues…
1CZT 1.87 Å, Crystal structure of the C2 domain of human coagulation factor V
1CZS 1.9 Å, Crystal structure of the C2 domain of human coagulation factor V: complex with…
1CZV 2.4 Å, Crystal structure of the C2 domain of human coagulation factor V: dimeric crystal form
3P70 2.55 Å, Structural basis of thrombin-mediated factor V activation: essential role of the…
9T00 2.8 Å, Crystal structure of prethrombin-2 with a peptide corresponding to the C-terminus of the…
36JB 2.9 Å, Coagulation factor V DTQQ, membrane-bound, on Ptd-choline : Ptd-serine 75:25 vesicles
9MOV 3.0 Å, Cryo-EM structure of factor Va bound to activated protein C
9TLE 3.1 Å, Structure of human prothrombinase with prothrombin
9TLG 3.1 Å, Structure of human prothrombinase with meizothrombin

Browse structure collections

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