6MF2: Improved Model of Human Coagulation Factor VIII

Improved Model of Human Coagulation Factor VIII. Determined by X-ray diffraction at 3.61 Å resolution. Released 11 Sept 2019.

Method: X-ray diffraction
Resolution: 3.61 Å
Organism: Homo sapiens
Chains: 1
Atoms: 10,035
Mol. weight: 175.84 kDa
Ligands: CA, CU1, ZN
Released: 11 Sept 2019

Explore 6MF2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MF2 contains 23 α-helices and 121 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: 23 helices, 121 β-strands

Element	Residues	Length	Sheet
β-strand	13-14	2	1
β-strand	46-47	2	1
β-strand	54	1	2
β-strand	62	1	2
α-helix	72	1
β-strand	73-78	6	3
β-strand	96	1	4
β-strand	99-100	2	3
β-strand	128	1	4
α-helix	129	1
β-strand	153-159	7	3
α-helix	164-169	6
β-strand	174-179	6	3
α-helix	180	1
β-strand	194-197	4	5
β-strand	201-203	3	6
β-strand	230-232	3	6
β-strand	234	1	7
β-strand	237	1	7
β-strand	246-247	2	8
β-strand	253-257	5	5
β-strand	258	1	9
β-strand	269-271	3	8
β-strand	276-278	3	5
β-strand	281-283	3	5
β-strand	286	1	8
β-strand	293	1	9
β-strand	296-298	3	5
β-strand	304-310	7	8
β-strand	322-326	5	8
β-strand	381	1	10
β-strand	384-394	11	11
α-helix	408-412	5
β-strand	422-430	9	11
β-strand	431	1	12
β-strand	439	1	12
β-strand	453	1	13
β-strand	456	1	13
β-strand	460-461	2	10
β-strand	463-468	6	11
β-strand	473	1	14
β-strand	476-477	2	13
β-strand	482	1	10
α-helix	484	1
β-strand	485	1	15
α-helix	498-500	3
β-strand	503	1	14
β-strand	508-510	3	11
β-strand	511	1	15
β-strand	513-514	2	10
α-helix	517-519	3
β-strand	528-534	7	13
α-helix	539-543	5
β-strand	548-554	7	13
β-strand	573-580	8	16
α-helix	581-583	3
α-helix	585-587	3
α-helix	588-594	7
α-helix	606-610	5
β-strand	613-617	5	16
β-strand	620	1	16
β-strand	626	1	17
β-strand	634-641	8	16
β-strand	649-653	5	18
β-strand	658-659	2	16
β-strand	664-665	2	16
β-strand	667-670	4	18
α-helix	671	1
β-strand	674-681	8	16
β-strand	689	1	17
β-strand	690-691	2	18
β-strand	705	1	17
β-strand	1697-1707	11	19
β-strand	1730-1737	8	19
β-strand	1766	1	20
β-strand	1770-1777	8	19
β-strand	1783	1	21
β-strand	1786	1	22
β-strand	1807	1	21
β-strand	1812-1818	7	19
β-strand	1832-1837	6	20
β-strand	1838	1	22
β-strand	1853-1858	6	20
β-strand	1874-1875	2	23
β-strand	1878-1880	3	24
β-strand	1883-1884	2	25
α-helix	1885-1887	3
α-helix	1893-1895	3
α-helix	1914-1916	3
β-strand	1917-1918	2	25
β-strand	1921	1	24
β-strand	1924	1	24
β-strand	1933-1934	2	26
β-strand	1940-1941	2	23
β-strand	1944-1946	3	24
α-helix	1950-1952	3
β-strand	1954-1957	4	27
β-strand	1958	1	26
β-strand	1963-1966	4	28
β-strand	1970-1973	4	28
β-strand	1975-1978	4	27
β-strand	1987	1	28
β-strand	1988	1	23
β-strand	1994-1998	5	26
α-helix	2003-2006	4
β-strand	2012-2016	5	26
β-strand	2023-2024	2	29
α-helix	2034-2036	3
β-strand	2038	1	30
α-helix	2048-2050	3
β-strand	2052	1	31
β-strand	2062-2064	3	32
β-strand	2071-2072	2	30
β-strand	2079-2084	6	29
β-strand	2088-2091	4	30
β-strand	2094-2106	13	30
β-strand	2113	1	30
β-strand	2138-2146	9	29
β-strand	2148-2157	10	30
β-strand	2160-2162	3	32
β-strand	2164	1	31
β-strand	2166-2169	4	29
β-strand	2177	1	33
α-helix	2187-2189	3
β-strand	2190-2192	3	34
α-helix	2205-2207	3
β-strand	2209	1	35
β-strand	2219	1	36
β-strand	2230-2233	4	34
β-strand	2238-2246	9	35
β-strand	2248-2249	2	37
β-strand	2254-2255	2	37
β-strand	2256-2257	2	38
β-strand	2260-2264	5	34
β-strand	2272-2273	2	34
β-strand	2275	1	39
β-strand	2280	1	39
β-strand	2283	1	34
β-strand	2293-2295	3	35
β-strand	2305-2310	6	34
β-strand	2313-2314	2	38
β-strand	2316	1	38
β-strand	2319	1	36
β-strand	2320-2327	8	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor VIII	A	protein	1512	Homo sapiens	P00451 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6MF2_1 Coagulation factor VIII (chains A)
SATRRYYLGAVELSWDYMQSDLGELPVDARFPPRVPKSFPFNTSVVYKKTLFVEFTDHLF
NIAKPRPPWMGLLGPTIQAEVYDTVVITLKNMASHPVSLHAVGVSYWKASEGAEYDDQTS
QREKEDDKVFPGGSHTYVWQVLKENGPMASDPLCLTYSYLSHVDLVKDLNSGLIGALLVC
REGSLAKEKTQTLHKFILLFAVFDEGKSWHSETKNSLMQDRDAASARAWPKMHTVNGYVN
RSLPGLIGCHRKSVYWHVIGMGTTPEVHSIFLEGHTFLVRNHRQASLEISPITFLTAQTL
LMDLGQFLLFCHISSHQHDGMEAYVKVDSCPEEPQLRMKNNEEAEDYDDDLTDSEMDVVR
FDDDNSPSFIQIRSVAKKHPKTWVHYIAAEEEDWDYAPLVLAPDDRSYKSQYLNNGPQRI
GRKYKKVRFMAYTDETFKTREAIQHESGILGPLLYGEVGDTLLIIFKNQASRPYNIYPHG
ITDVRPLYSRRLPKGVKHLKDFPILPGEIFKYKWTVTVEDGPTKSDPRCLTRYYSSFVNM
ERDLASGLIGPLLICYKESVDQRGNQIMSDKRNVILFSVFDENRSWYLTENIQRFLPNPA
GVQLEDPEFQASNIMHSINGYVFDSLQLSVCLHEVAYWYILSIGAQTDFLSVFFSGYTFK
HKMVYEDTLTLFPFSGETVFMSMENPGLWILGCHNSDFRNRGMTALLKVSSCDKNTGDYY
EDSYEDISAYLLSKNNAIEPRSDPLAWDNHYGTQIPKEEWKSQEKSPEKTAFKKKDTILS
LNACESNHAIAAINEGQNKPEIEVTWAKQGRTERLCSQNPPVLKRHQREITRTTLQSDQE
EIDYDDTISVEMKKEDFDIYDEDENQSPRSFQKKTRHYFIAAVERLWDYGMSSSPHVLRN
RAQSGSVPQFKKVVFQEFTDGSFTQPLYRGELNEHLGLLGPYIRAEVEDNIMVTFRNQAS
RPYSFYSSLISYEEDQRQGAEPRKNFVKPNETKTYFWKVQHHMAPTKDEFDCKAWAYFSD
VDLEKDVHSGLIGPLLVCHTNTLNPAHGRQVTVQEFALFFTIFDETKSWYFTENMERNCR
APCNIQMEDPTFKENYRFHAINGYIMDTLPGLVMAQDQRIRWYLLSMGSNENIHSIHFSG
HVFTVRKKEEYKMALYNLYPGVFETVEMLPSKAGIWRVECLIGEHLHAGMSTLFLVYSNK
CQTPLGMASGHIRDFQITASGQYGQWAPKLARLHYSGSINAWSTKEPFSWIKVDLLAPMI
IHGIKTQGARQKFSSLYISQFIIMYSLDGKKWQTYRGNSTGTLMVFFGNVDSSGIKHNIF
NPPIIARYIRLHPTHYSIRSTLRMELMGCDLNSCSMPLGMESKAISDAQITASSYFTNMF
ATWSPSKARLHLQGRSNAWRPQVNNPKEWLQVDFQKTMKVTGVTTQGVKSLLTSMYVKEF
LISSSQDGHQWTLFFQNGKVKVFQGNQDSFTPVVNSLDPPLLTRYLRIHPQSWVHQIALR
MEVLGCEAQDLY

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
CU1	Copper (I) ion	Cu	1
ZN	Zinc ion	Zn	1

Primary citation

The 3.2 angstrom structure of a bioengineered variant of blood coagulation factor VIII indicates two conformations of the C2 domain. Smith, I.W., d'Aquino, A.E., Coyle, C.W. et al. J Thromb Haemost (2020) 18:57-69. DOI 10.1111/jth.14621 · PubMed

Other PDB entries of the same protein (UniProt P00451 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3HNY 1.07 Å, Factor VIII Trp2313-His2315 segment is involved in membrane binding as shown by crystal…
3HNB 1.15 Å, Factor VIII Trp2313-His2315 segment is involved in membrane binding as shown by crystal…
1D7P 1.5 Å, Crystal structure of the c2 domain of human factor viii at 1.5 a resolution at 1.5 A
9D5D 1.83 Å, Crystal Structure of Blood Coagulation Factor VIII C2 Domain Mutant L2251A/L2252A
1IQD 2.0 Å, Human Factor VIII C2 Domain complexed to human monoclonal BO2C11 Fab.
3HOB 2.07 Å, Factor VIII Trp2313-His2315 segment is involved in membrane binding as shown by crystal…
4PT6 2.1 Å, The discobody: an engineered discoidin domain from factor VIII that binds v 3 integrin…
4KI5 2.47 Å, Cystal structure of human factor VIII C2 domain in a ternary complex with murine…
4XZU 2.61 Å, Crystal Structure of the Human Factor VIII C2 Domain in Complex with Murine 3E6…
7KWO 2.9 Å, Rfviiifc-vwf-xten (BIVV001)
36JL 3.15 Å, Coagulation factor VIII, full-length, membrane-bound, on Ptd-choline : Ptd-serine 75:25…
9JBV 3.17 Å, Structure of Engineered Coagulation Factor VIII with Enhanced Secretion and Coagulation…

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