4KI5: Murine monoclonal 3E6 FAB heavy chain

Cystal structure of human factor VIII C2 domain in a ternary complex with murine inhbitory antibodies 3E6 and G99. Determined by X-ray diffraction at 2.47 Å resolution. Released 15 Jan 2014.

Method: X-ray diffraction
Resolution: 2.47 Å
Organisms: Mus musculus, Homo sapiens
Chains: 5
Atoms: 8,074
Mol. weight: 115.2 kDa
Released: 15 Jan 2014

Explore 4KI5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KI5 contains 33 α-helices and 103 β-strands across 5 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 C: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	10-12	3	2
β-strand	18-24	7	1
α-helix	27-31	5
β-strand	34-39	6	2
β-strand	46-51	6	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
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	130-132	3
β-strand	135	1	4
β-strand	138-148	11	4
β-strand	149	1	3
β-strand	154-157	4	5
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 D: 7 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
β-strand	113-117	5	9
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	9
β-strand	139	1	8
β-strand	144-149	6	10
β-strand	152-154	3	10
β-strand	158-162	5	9
β-strand	172-181	10	9
α-helix	182-185	4
β-strand	190-196	7	10
β-strand	204-209	6	10

Chain E: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
α-helix	7-9	3
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	32-39	8	12
β-strand	45-52	8	12
β-strand	57-60	4	12
α-helix	62-64	3
β-strand	68-73	6	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-100	9	12
β-strand	116-120	5	12
α-helix	123-125	3
β-strand	126	1	13
β-strand	129-133	5	14
α-helix	136-138	3
β-strand	141	1	14
β-strand	144-154	11	14
β-strand	155	1	13
β-strand	160-163	4	15
α-helix	164-166	3
β-strand	168	1	15
β-strand	172-174	3	14
α-helix	175-177	3
β-strand	178-180	3	14
β-strand	183-193	11	14
β-strand	203-208	6	15
α-helix	209-211	3
β-strand	213-218	6	15
α-helix	219	1

Chain F: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-14	5	17
β-strand	19-25	7	16
β-strand	33-38	6	17
β-strand	44-49	6	17
β-strand	53-54	2	17
α-helix	55	1
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	84-90	7	17
α-helix	96	1
β-strand	97-98	2	17
β-strand	102-107	6	17
β-strand	111	1	18
β-strand	114-118	5	19
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	19
β-strand	140	1	18
β-strand	145-150	6	20
β-strand	153-155	3	20
β-strand	159-163	5	19
β-strand	173-182	10	19
α-helix	183-186	4
β-strand	191-197	7	20
β-strand	205-210	6	20

Chain M: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	2176-2177	2	21
α-helix	2187-2189	3
β-strand	2190-2192	3	21
β-strand	2197	1	22
β-strand	2202	1	22
α-helix	2205-2207	3
β-strand	2209	1	21
β-strand	2219	1	23
β-strand	2230-2246	17	21
β-strand	2248-2250	3	24
β-strand	2253-2255	3	24
β-strand	2256-2265	10	21
β-strand	2272-2273	2	21
β-strand	2275-2276	2	25
β-strand	2279-2280	2	25
β-strand	2283-2284	2	21
β-strand	2293-2314	22	21
β-strand	2319	1	23
β-strand	2320-2326	7	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Murine monoclonal 3E6 FAB heavy chain	C	protein	219	Mus musculus
Murine monoclonal 3E6 FAB light chain	D	protein	213	Mus musculus
Murine monoclonal G99 FAB heavy chain	E	protein	224	Mus musculus
Murine monoclonal G99 FAB light chain	F	protein	214	Mus musculus
Coagulation factor VIII	M	protein	183	Homo sapiens	P00451 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>4KI5_1 MURINE MONOCLONAL 3E6 FAB HEAVY CHAIN (chains C)
QIQLVQSGPELKKPGKTVKISCKASDYTFTDYSLHWVKQAPGKGLKWMGWINTETGDPAY
ADDFKGRFAFSLETSVRTAYLQINNLKNEDTAIYFCAREDDGLASWGQGTTLTVSSAKTT
APSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTL
SSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPA

Sequence of entity 2 (D), FASTA

>4KI5_2 MURINE MONOCLONAL 3E6 FAB LIGHT CHAIN (chains D)
QIVLTQSPAIMSASPGEKVTMTCSASSTVSYMYWYQQKPGSSPRFLISDTSNLASGVPVR
FSGSGSGTSYSLTISRIEAEDAATYYCQHWSSYPLTFGGGTKLELKRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (E), FASTA

>4KI5_3 MURINE MONOCLONAL G99 FAB HEAVY CHAIN (chains E)
QVQLQQSGAELMKPGASVKISCKATGYTFSSYWIEWVKQRPGHGLEWIGEILPGSGSTNY
NERFKGKASFTADSSSNTAYMQLSSLTSEDSAVYYCTRTSYYFGSSYDFDVWGAGTTVTV
SSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQ
SDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGP

Sequence of entity 4 (F), FASTA

>4KI5_4 MURINE MONOCLONAL G99 FAB LIGHT CHAIN (chains F)
DIQMTQSPSSLSASLGERVSLTCRASQEISGYLSWLQQKPDGTIKRLIYAASTLDSSVPK
RFSGSRSGSDYSLTISSLDSEDFAVYYCLQYASYPYTFGGGTKVEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 5 (M), FASTA

>4KI5_5 Coagulation factor VIII (chains M)
MGSSHHHHHHSSGLVPRGSHMLNSCSMPLGMESKAISDAQITASSYFTNMFATWSPSKAR
LHLQGRSNAWRPQVNNPKEWLQVDFQKTMKVTGVTTQGVKSLLTSMYVKEFLISSSQDGH
QWTLFFQNGKVKVFQGNQDSFTPVVNSLDPPLLTRYLRIHPQSWVHQIALRMEVLGCEAQ
DLY

Primary citation

Structure of the factor VIII C2 domain in a ternary complex with 2 inhibitor antibodies reveals classical and nonclassical epitopes. Walter, J.D., Werther, R.A., Brison, C.M. et al. Blood (2013) 122:4270-4278. DOI 10.1182/blood-2013-08-519124 · 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…
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…
6MF0 3.2 Å, Crystal Structure Determination of Human/Porcine Chimera Coagulation Factor VIII

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