4XZU: Human Factor VIII C2 Domain

Crystal Structure of the Human Factor VIII C2 Domain in Complex with Murine 3E6 Inhibitory Antibody. Determined by X-ray diffraction at 2.61 Å resolution. Released 9 Dec 2015.

Method: X-ray diffraction
Resolution: 2.61 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 9,034
Mol. weight: 128.79 kDa
Ligands: MG
Released: 9 Dec 2015

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

Secondary structure: helices and β-sheets

4XZU contains 34 α-helices and 120 β-strands across 6 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: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	10-12	3	2
β-strand	18-24	7	1
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	103-106	4	2
β-strand	110-114	5	2
α-helix	117-119	3
β-strand	120	1	3
α-helix	121-122	2
β-strand	123-127	5	4
α-helix	128-130	3
β-strand	138-148	11	4
β-strand	149	1	3
β-strand	154-157	4	5
α-helix	158-160	3
β-strand	162	1	5
β-strand	166-173	8	4
β-strand	178-187	10	4
β-strand	197-202	6	5
α-helix	203-205	3
β-strand	207-212	6	5

Chain B: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	33-37	5	7
β-strand	44-48	5	7
β-strand	52-53	2	7
α-helix	54	1
β-strand	61-66	6	6
β-strand	69-74	6	6
α-helix	79-81	3
β-strand	83-89	7	7
α-helix	95	1
β-strand	96-97	2	7
β-strand	101-105	5	7
α-helix	106	1
β-strand	110	1	8
α-helix	111-112	2
β-strand	113-117	5	9
α-helix	121-124	4
β-strand	128-138	11	9
β-strand	139	1	8
β-strand	143-149	7	10
β-strand	152-154	3	10
β-strand	158-162	5	9
α-helix	163-166	4
β-strand	172-181	10	9
α-helix	182-185	4
β-strand	190-197	8	10
α-helix	203	1
β-strand	204-209	6	10

Chain E: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	16
β-strand	10-12	3	17
β-strand	18-24	7	16
α-helix	29-31	3
β-strand	34-39	6	17
β-strand	46-51	6	17
β-strand	58-60	3	17
α-helix	62-64	3
β-strand	68-73	6	16
α-helix	74-76	3
β-strand	78-83	6	16
α-helix	88-90	3
β-strand	92-99	8	17
β-strand	103-106	4	17
β-strand	110-114	5	17
β-strand	120	1	18
β-strand	123-126	4	19
β-strand	138-148	11	19
β-strand	149	1	18
β-strand	154-157	4	20
β-strand	162	1	20
β-strand	166-168	3	19
α-helix	169-171	3
β-strand	172-173	2	19
β-strand	178-187	10	19
β-strand	197-202	6	20
α-helix	203-205	3
β-strand	207-212	6	20

Chain F: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	21
β-strand	10-13	4	22
β-strand	19-25	7	21
β-strand	33-37	5	22
β-strand	44-48	5	22
β-strand	52-53	2	22
α-helix	54	1
β-strand	61-66	6	21
β-strand	69-74	6	21
α-helix	79-81	3
β-strand	83-89	7	22
α-helix	95	1
β-strand	96-97	2	22
β-strand	101-105	5	22
α-helix	106	1
β-strand	110	1	23
β-strand	113-117	5	24
α-helix	121-126	6
β-strand	128-138	11	24
β-strand	139	1	23
β-strand	144	1	25
β-strand	147	1	26
β-strand	158-162	5	24
β-strand	172-181	10	24
α-helix	182-185	4
β-strand	193	1	26
β-strand	196	1	25

Chain G: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2176-2177	2	27
α-helix	2187-2189	3
β-strand	2190-2192	3	27
β-strand	2197	1	28
β-strand	2202	1	28
α-helix	2205-2207	3
β-strand	2209	1	27
β-strand	2219	1	29
β-strand	2230-2246	17	27
β-strand	2248-2250	3	30
β-strand	2253-2255	3	30
β-strand	2256-2265	10	27
β-strand	2272-2273	2	27
β-strand	2275-2276	2	31
β-strand	2279-2280	2	31
β-strand	2283-2284	2	27
α-helix	2291-2292	2
β-strand	2293-2295	3	27
β-strand	2301-2314	14	27
β-strand	2319	1	29
β-strand	2320-2326	7	27

Chain M: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	2176-2177	2	11
α-helix	2187-2189	3
β-strand	2190-2192	3	11
β-strand	2196-2197	2	12
β-strand	2202-2203	2	12
α-helix	2205-2207	3
β-strand	2209	1	11
β-strand	2219	1	13
β-strand	2230-2246	17	11
β-strand	2248-2250	3	14
β-strand	2253-2255	3	14
β-strand	2256-2265	10	11
β-strand	2272-2273	2	11
β-strand	2275-2276	2	15
β-strand	2279-2280	2	15
α-helix	2281	1
β-strand	2283-2284	2	11
β-strand	2293-2314	22	11
β-strand	2319	1	13
β-strand	2320-2326	7	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
3E6 antibody Fab heavy chain	A, E	protein	219	Mus musculus
3E6 antibody Fab light chain	B, F	protein	213	Mus musculus
Coagulation factor VIII	G, M	protein	154	Homo sapiens	P00451 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>4XZU_1 3E6 antibody Fab heavy chain (chains A, E)
QIQLVQSGPELKKPGKTVKISCKASDYTFTDYSLHWVKQAPGKGLKWMGWINTETGDPAY
ADDFKGRFAFSLETSVRTAYLQINNLKNEDTAIYFCAREDDGLASWGQGTTLTVSSAKTT
APSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTL
SSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPA

Sequence of entity 2 (B, F), FASTA

>4XZU_2 3E6 antibody Fab light chain (chains B, F)
QIVLTQSPAIMSASPGEKVTMTCSASSTVSYMYWYQQKPGSSPRFLISDTSNLASGVPVR
FSGSGSGTSYSLTISRIEAEDAATYYCQHWSSYPLTFGGGTKLELKRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHSTSTSPIVKSFNRNEC

Sequence of entity 3 (G, M), FASTA

>4XZU_3 Coagulation factor VIII (chains G, M)
CSMPLGMESKAISDAQITASSYFTNMFATWSPSKARLHLQGRSNAWRPQVNNPKEWLQVD
FQKTMKVTGVTTQGVKSLLTSMYVKEFLISSSQDGHQWTLFFQNGKVKVFQGNQDSFTPV
VNSLDPPLLTRYLRIHPQSWVHQIALRMEVLGCE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3

Primary citation

Structure of the Human Factor VIII C2 Domain in Complex with the 3E6 Inhibitory Antibody. Wuerth, M.E., Cragerud, R.K., Clint Spiegel, P. Sci Rep (2015) 5:17216-17216. DOI 10.1038/srep17216 · 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…
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…
6MF0 3.2 Å, Crystal Structure Determination of Human/Porcine Chimera Coagulation Factor VIII

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