7K66: Blood Coagulation Factor VIII

Structure of Blood Coagulation Factor VIII in Complex with an Anti-C1 Domain Pathogenic Antibody Inhibitor. Determined by X-ray diffraction at 3.92 Å resolution. Released 14 Oct 2020.

Method: X-ray diffraction
Resolution: 3.92 Å
Organisms: Sus scrofa, Homo sapiens, Mus musculus
Chains: 3
Atoms: 13,606
Mol. weight: 217.29 kDa
Ligands: ZN, CA, CU, NAG
Released: 14 Oct 2020

Explore 7K66 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7K66 contains 29 α-helices and 160 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 A: 24 helices, 116 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	1
β-strand	47-54	8	1
β-strand	55	1	2
β-strand	63	1	2
α-helix	73-75	3
β-strand	76-77	2	3
β-strand	85-91	7	1
β-strand	97	1	4
β-strand	100-101	2	5
α-helix	121-127	7
β-strand	129	1	4
β-strand	136	1	1
β-strand	139	1	1
β-strand	154-155	2	6
β-strand	159-160	2	5
α-helix	165-171	7
β-strand	176-177	2	3
β-strand	179-180	2	6
β-strand	196-198	3	7
β-strand	202-204	3	8
α-helix	205-207	3
β-strand	231-233	3	8
β-strand	247-248	2	9
β-strand	254-259	6	7
β-strand	268-272	5	9
β-strand	275	1	9
β-strand	277	1	10
β-strand	284	1	10
β-strand	286-289	4	9
β-strand	294-299	6	7
β-strand	305-311	7	9
β-strand	322-327	6	9
α-helix	378-380	3
β-strand	381-389	9	11
β-strand	390-394	5	12
α-helix	407-410	4
β-strand	422-426	5	12
β-strand	429-431	3	11
β-strand	439	1	11
β-strand	453	1	13
β-strand	460-468	9	11
β-strand	473	1	14
β-strand	476-477	2	13
β-strand	483-485	3	11
α-helix	498-500	3
α-helix	502	1
β-strand	503	1	14
α-helix	504	1
β-strand	508-514	7	11
β-strand	529-534	6	13
α-helix	539-545	7
β-strand	549-553	5	13
β-strand	573-580	8	15
α-helix	581-583	3
α-helix	588-594	7
α-helix	609-611	3
β-strand	613-617	5	15
β-strand	620	1	15
β-strand	626	1	16
β-strand	634-641	8	15
β-strand	649-652	4	17
β-strand	658-659	2	15
β-strand	664-665	2	15
β-strand	667-670	4	17
β-strand	674-681	8	15
α-helix	696-699	4
β-strand	705	1	16
β-strand	1695-1703	9	18
β-strand	1706-1707	2	19
β-strand	1730-1731	2	19
β-strand	1734-1737	4	18
α-helix	1751-1753	3
β-strand	1763-1765	3	20
β-strand	1770-1777	8	18
β-strand	1783	1	21
β-strand	1786	1	20
β-strand	1807	1	21
β-strand	1812-1818	7	18
α-helix	1819-1820	2
α-helix	1825-1826	2
β-strand	1832-1838	7	20
α-helix	1845-1849	5
β-strand	1852-1858	7	20
β-strand	1874-1875	2	22
β-strand	1878-1879	2	22
β-strand	1880-1884	5	23
α-helix	1885-1887	3
β-strand	1917-1921	5	23
β-strand	1924	1	23
β-strand	1933-1934	2	24
β-strand	1940-1945	6	22
β-strand	1954-1958	5	24
β-strand	1963	1	25
β-strand	1964-1965	2	22
β-strand	1966-1967	2	26
β-strand	1969-1970	2	26
β-strand	1973	1	25
β-strand	1975-1978	4	24
β-strand	1983-1988	6	22
β-strand	1994-2000	7	24
α-helix	2003-2006	4
β-strand	2011-2016	6	24
β-strand	2023-2024	2	27
β-strand	2037-2040	4	27
α-helix	2048-2051	4
β-strand	2052	1	27
β-strand	2062	1	28
β-strand	2070-2087	18	27
β-strand	2089-2091	3	29
β-strand	2094-2096	3	29
β-strand	2097	1	30
β-strand	2098-2105	8	27
β-strand	2113-2114	2	27
α-helix	2125	1
β-strand	2126-2127	2	27
β-strand	2136-2156	21	27
β-strand	2157	1	31
β-strand	2159	1	31
β-strand	2160	1	30
β-strand	2162	1	28
β-strand	2163-2169	7	27
β-strand	2176-2177	2	32
α-helix	2187-2189	3
β-strand	2190-2192	3	32
β-strand	2197	1	33
β-strand	2202	1	33
α-helix	2205-2207	3
β-strand	2209	1	32
β-strand	2219	1	34
β-strand	2230-2246	17	32
β-strand	2248-2250	3	35
β-strand	2253-2255	3	35
β-strand	2256-2265	10	32
β-strand	2272-2273	2	32
β-strand	2275-2277	3	36
β-strand	2279-2280	2	36
β-strand	2283-2284	2	32
β-strand	2293-2314	22	32
β-strand	2319	1	34
β-strand	2320-2327	8	32

Chain B: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	37
α-helix	7-9	3
β-strand	18	1	38
β-strand	22-23	2	37
β-strand	35-39	5	39
β-strand	46-50	5	39
β-strand	51-52	2	40
β-strand	57-58	2	40
β-strand	72-73	2	41
β-strand	78-79	2	41
β-strand	83	1	38
β-strand	93-94	2	39
β-strand	128	1	42
β-strand	143-145	3	43
β-strand	149	1	42
β-strand	150-152	3	44
β-strand	158-161	4	45
α-helix	172-174	3
β-strand	182-183	2	44
β-strand	188-190	3	43
β-strand	201	1	46
β-strand	202-205	4	45
β-strand	212-213	2	45
β-strand	216	1	46

Chain C: 3 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	47
β-strand	7	1	48
β-strand	10-12	3	49
β-strand	19-29	11	48
β-strand	32-37	6	49
β-strand	44-48	5	49
α-helix	52	1
β-strand	53	1	49
α-helix	54	1
β-strand	61	1	48
β-strand	65-74	10	48
β-strand	84-89	6	49
β-strand	102-104	3	49
β-strand	110	1	50
α-helix	111-112	2
β-strand	113-116	4	51
β-strand	131-138	8	51
β-strand	139	1	50
β-strand	147-148	2	52
β-strand	149	1	53
β-strand	152	1	53
β-strand	161-162	2	51
β-strand	172-178	7	51
β-strand	192-193	2	52
β-strand	206	1	52

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII	A	protein	1467	Sus scrofa, Homo sapiens	P00451 (AlphaFold model), P12263 (AlphaFold model)
2A9 heavy chain	B	protein	223	Mus musculus
2A9 light chain	C	protein	213	Mus musculus

Sequence of entity 1 (A), FASTA

>7K66_1 Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII,Coagulation factor VIII (chains A)
MQLELSTCVFLCLLPLGFSAIRRYYLGAVELSWDYRQSELLRELHVDTRFPATAPGALPL
GPSVLYKKTVFVEFTDQLFSVARPRPPWMGLLGPTIQAEVYDTVVVTLKNMASHPVSLHA
VGVSFWKSSEGAEYEDHTSQREKEDDKVLPGKSQTYVWQVLKENGPTASDPPCLTYSYLS
HVDLVKDLNSGLIGALLVCREGSLTRERTQNLHEFVLLFAVFDEGKSWHSARNDSWTRAM
DPAPARAQPAMHTVNGYVNRSLPGLIGCHKKSVYWHVIGMGTSPEVHSIFLEGHTFLVRH
HRQASLEISPLTFLTAQTFLMDLGQFLLFCHISSHHHGGMEAHVRVESCAEEPQLRRKAD
EEEDYDDNLYDSDMDVVRLDGDDVSPFIQIRSVAKKHPKTWVHYIAAEEEDWDYAPLVLA
PDDRSYKSQYLNNGPQRIGRKYKKVRFMAYTDETFKTREAIQHESGILGPLLYGEVGDTL
LIIFKNQASRPYNIYPHGITDVRPLYSRRLPKGVKHLKDFPILPGEIFKYKWTVTVEDGP
TKSDPRCLTRYYSSFVNMERDLASGLIGPLLICYKESVDQRGNQIMSDKRNVILFSVFDE
NRSWYLTENIQRFLPNPAGVQLEDPEFQASNIMHSINGYVFDSLQLSVCLHEVAYWYILS
IGAQTDFLSVFFSGYTFKHKMVYEDTLTLFPFSGETVFMSMENPGLWILGCHNSDFRNRG
MTALLKVSSCDKNTGDYYEDSYEDISAYLLSKNNAIEPRSFAQNSRPPSASAPKPPVLRR
HQRDISLPTFQPEEDKMDYDDIFSTETKGEDFDIYGEDENQDPRSFQKRTRHYFIAAVEQ
LWDYGMSESPRALRNRAQNGEVPRFKKVVFREFADGSFTQPSYRGELNKHLGLLGPYIRA
EVEDNIMVTFKNQASRPYSFYSSLISYPDDQEQGAEPRHNFVQPNETRTYFWKVQHHMAP
TEDEFDCKAWAYFSDVDLEKDVHSGLIGPLLICRANTLNAAHGRQVTVQEFALFFTIFDE
TKSWYFTENVERNCRAPCHLQMEDPTLKENYRFHAINGYVMDTLPGLVMAQNQRIRWYLL
SMGSNENIHSIHFSGHVFSVRKKEEYKMAVYNLYPGVFETVEMLPSKVGIWRIECLIGEH
LQAGMSTTFLVYSKKCQTPLGMASGHIRDFQITASGQYGQWAPKLARLHYSGSINAWSTK
EPFSWIKVDLLAPMIIHGIKTQGARQKFSSLYISQFIIMYSLDGKKWQTYRGNSTGTLMV
FFGNVDSSGIKHNIFNPPIIARYIRLHPTHYSIRSTLRMELMGCDLNSCSMPLGMESKAI
SDAQITASSYFTNMFATWSPSKARLHLQGRSNAWRPQVNNPKEWLQVDFQKTMKVTGVTT
QGVKSLLTSMYVKEFLISSSQDGHQWTLFFQNGKVKVFQGNQDSFTPVVNSLDPPLLTRY
LRIHPQSWVHQIALRMEVLGCEAQDLY

Sequence of entity 2 (B), FASTA

>7K66_2 2A9 heavy chain (chains B)
QIQLVQSGPELKKPGETVKISCKASGYTFTDYSMHWVKQAPGKGLKWMGWINTETGEPTY
ADDFKGRFAFSLETSASSAYLQINNLKNEDTATYFCARCGNYVDYAIDYWGQGTSVTVSS
AKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPA

Sequence of entity 3 (C), FASTA

>7K66_3 2A9 light chain (chains C)
ENVLTQSPAIMSASLGEKVTMSCRATSSVNYMYWYQQKSDASPKLWIFFTSSLAPGVPAR
FSGSGSGNSYSLTISSVEGEAAATYYCQQFTSSPFGSGTKLEIKAKRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHSTKTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
CA	Calcium ion	Ca	1
CU	Copper (II) ion	Cu	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Structure of blood coagulation factor VIII in complex with an anti-C1 domain pathogenic antibody inhibitor. Gish, J.S., Jarvis, L., Childers, K.C. et al. Blood (2021) 137:2981-2986. DOI 10.1182/blood.2020008940 · 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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