4BDV: Truncated B-domain human factor VIII

Crystal structure of a truncated B-domain human factor VIII. Determined by X-ray diffraction at 3.98 Å resolution. Released 15 May 2013.

Method: X-ray diffraction
Resolution: 3.98 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 9,973
Mol. weight: 167.98 kDa
Ligands: CU1, CA, ZN
Released: 15 May 2013

Explore 4BDV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4BDV contains 22 α-helices and 113 β-strands across 2 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: 14 helices, 60 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
β-strand	10-11	2	2
β-strand	49-50	2	2
β-strand	73-79	7	3
β-strand	83-86	4	1
β-strand	87-88	2	4
β-strand	96	1	5
β-strand	99-101	3	3
β-strand	104	1	1
β-strand	112	1	6
α-helix	120-122	3
β-strand	128	1	5
α-helix	129	1
β-strand	134-135	2	4
β-strand	138-139	2	1
α-helix	146-147	2
β-strand	153-159	7	3
β-strand	161	1	6
α-helix	165-171	7
β-strand	173-179	7	3
β-strand	183	1	7
β-strand	186	1	7
β-strand	193-195	3	8
β-strand	198-200	3	8
β-strand	234	1	9
β-strand	237	1	9
β-strand	246	1	10
β-strand	253-260	8	8
β-strand	269-271	3	10
β-strand	276-278	3	8
β-strand	281-283	3	8
β-strand	286	1	10
β-strand	293-297	5	8
β-strand	304-310	7	10
α-helix	313-315	3
β-strand	321-326	6	10
α-helix	327-330	4
α-helix	378-380	3
β-strand	381-394	14	11
β-strand	415	1	12
β-strand	418	1	12
β-strand	422-431	10	11
β-strand	439	1	11
α-helix	441-442	2
β-strand	453-456	4	13
β-strand	460-468	9	11
β-strand	473	1	14
β-strand	476-478	3	13
β-strand	482-485	4	11
β-strand	503	1	14
β-strand	508-514	7	11
α-helix	517-519	3
β-strand	529-534	6	13
α-helix	541-544	4
β-strand	548-554	7	13
β-strand	572-580	9	15
α-helix	581-583	3
α-helix	587-594	8
α-helix	606-610	5
β-strand	613-617	5	15
β-strand	620	1	15
β-strand	626-629	4	16
β-strand	635-641	7	15
β-strand	649-650	2	17
β-strand	651	1	18
β-strand	658-659	2	15
β-strand	664-665	2	15
β-strand	669-670	2	17
β-strand	675-680	6	15
β-strand	686-690	5	16
β-strand	692	1	18
α-helix	697-699	3
β-strand	701	1	15
β-strand	704-708	5	16

Chain B: 8 helices, 53 β-strands

Element	Residues	Length	Sheet
β-strand	1695-1706	12	19
β-strand	1731-1737	7	19
β-strand	1738	1	20
β-strand	1746	1	20
α-helix	1760-1761	2
β-strand	1763-1766	4	21
β-strand	1770-1777	8	19
β-strand	1783	1	22
β-strand	1787	1	21
β-strand	1807	1	22
β-strand	1811-1818	8	19
α-helix	1821-1823	3
β-strand	1832-1838	7	21
α-helix	1845-1848	4
β-strand	1852-1858	7	21
α-helix	1864	1
β-strand	1874-1880	7	23
β-strand	1883-1884	2	24
β-strand	1917-1918	2	24
β-strand	1921	1	23
β-strand	1924	1	23
β-strand	1933-1935	3	25
β-strand	1940-1946	7	23
β-strand	1955-1958	4	25
β-strand	1963-1965	3	23
β-strand	1971-1973	3	23
β-strand	1975-1977	3	25
α-helix	1978-1979	2
β-strand	1980	1	23
β-strand	1984-1988	5	23
β-strand	1994-2000	7	25
α-helix	2003-2006	4
β-strand	2012-2017	6	25
β-strand	2023-2024	2	26
β-strand	2037-2039	3	26
β-strand	2052	1	26
β-strand	2062-2064	3	27
β-strand	2071-2086	16	26
β-strand	2088-2090	3	28
β-strand	2095-2097	3	28
β-strand	2098-2106	9	26
β-strand	2113-2114	2	26
β-strand	2125-2127	3	26
β-strand	2137-2156	20	26
β-strand	2160-2162	3	27
β-strand	2164-2169	6	26
β-strand	2176-2177	2	29
α-helix	2187-2189	3
β-strand	2190-2192	3	29
β-strand	2197	1	30
β-strand	2202	1	30
α-helix	2205-2207	3
β-strand	2219	1	31
β-strand	2230-2245	16	29
β-strand	2247-2249	3	32
β-strand	2254-2256	3	32
β-strand	2259-2265	7	29
β-strand	2282-2284	3	29
β-strand	2293-2312	20	29
β-strand	2319	1	31
β-strand	2321-2327	7	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Factor viiia heavy chain, 92 kda isoform, B domain	A	protein	760	HOMO SAPIENS	P00451 (AlphaFold model)
Factor viiia light chain	B	protein	685	HOMO SAPIENS	P00451 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4BDV_1 FACTOR VIIIA HEAVY CHAIN, 92 KDA ISOFORM, B DOMAIN (chains A)
ATRRYYLGAVELSWDYMQSDLGELPVDARFPPRVPKSFPFNTSVVYKKTLFVEFTDHLFN
IAKPRPPWMGLLGPTIQAEVYDTVVITLKNMASHPVSLHAVGVSYWKASEGAEYDDQTSQ
REKEDDKVFPGGSHTYVWQVLKENGPMASDPLCLTYSYLSHVDLVKDLNSGLIGALLVCR
EGSLAKEKTQTLHKFILLFAVFDEGKSWHSETKNSLMQDRDAASARAWPKMHTVNGYVNR
SLPGLIGCHRKSVYWHVIGMGTTPEVHSIFLEGHTFLVRNHRQASLEISPITFLTAQTLL
MDLGQFLLFCHISSHQHDGMEAYVKVDSCPEEPQLRMKNNEEAEDYDDDLTDSEMDVVRF
DDDNSPSFIQIRSVAKKHPKTWVHYIAAEEEDWDYAPLVLAPDDRSYKSQYLNNGPQRIG
RKYKKVRFMAYTDETFKTREAIQHESGILGPLLYGEVGDTLLIIFKNQASRPYNIYPHGI
TDVRPLYSRRLPKGVKHLKDFPILPGEIFKYKWTVTVEDGPTKSDPRCLTRYYSSFVNME
RDLASGLIGPLLICYKESVDQRGNQIMSDKRNVILFSVFDENRSWYLTENIQRFLPNPAG
VQLEDPEFQASNIMHSINGYVFDSLQLSVCLHEVAYWYILSIGAQTDFLSVFFSGYTFKH
KMVYEDTLTLFPFSGETVFMSMENPGLWILGCHNSDFRNRGMTALLKVSSCDKNTGDYYE
DSYEDISAYLLSKNNAIEPRSFSQNSRHPSQNPPVLKRHQ

Sequence of entity 2 (B), FASTA

>4BDV_2 FACTOR VIIIA LIGHT CHAIN (chains B)
REITRTTLQSDQEEIDYDDTISVEMKKEDFDIYDEDENQSPRSFQKKTRHYFIAAVERLW
DYGMSSSPHVLRNRAQSGSVPQFKKVVFQEFTDGSFTQPLYRGELNEHLGLLGPYIRAEV
EDNIMVTFRNQASRPYSFYSSLISYEEDQRQGAEPRKNFVKPNETKTYFWKVQHHMAPTK
DEFDCKAWAYFSDVDLEKDVHSGLIGPLLVCHTNTLNPAHGRQVTVQEFALFFTIFDETK
SWYFTENMERNCRAPCNIQMEDPTFKENYRFHAINGYIMDTLPGLVMAQDQRIRWYLLSM
GSNENIHSIHFSGHVFTVRKKEEYKMALYNLYPGVFETVEMLPSKAGIWRVECLIGEHLH
AGMSTLFLVYSNKCQTPLGMASGHIRDFQITASGQYGQWAPKLARLHYSGSINAWSTKEP
FSWIKVDLLAPMIIHGIKTQGARQKFSSLYISQFIIMYSLDGKKWQTYRGNSTGTLMVFF
GNVDSSGIKHNIFNPPIIARYIRLHPTHYSIRSTLRMELMGCDLNSCSMPLGMESKAISD
AQITASSYFTNMFATWSPSKARLHLQGRSNAWRPQVNNPKEWLQVDFQKTMKVTGVTTQG
VKSLLTSMYVKEFLISSSQDGHQWTLFFQNGKVKVFQGNQDSFTPVVNSLDPPLLTRYLR
IHPQSWVHQIALRMEVLGCEAQDLY

Ligands and cofactors

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

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

Primary citation

Evaluation of the Metal Binding Sites in a Recombinant Coagulation Factor Viii Identifies Two Sites with Unique Metal Binding Properties. Svensson, L.A., Thim, L., Olsen, O.H. et al. Biol Chem (2013) 394:761. DOI 10.1515/HSZ-2012-0298 · 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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