1PG7: Murine 6A6 Fab

Murine 6A6 Fab in complex with humanized anti-Tissue Factor D3H44 Fab. Determined by X-ray diffraction at 2.5 Å resolution. Released 26 Aug 2003.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Mus musculus, Homo sapiens
Chains: 8
Atoms: 13,317
Mol. weight: 185.71 kDa
Released: 26 Aug 2003

Explore 1PG7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1PG7 contains 69 α-helices and 185 β-strands across 8 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 H: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	33-39	7	2
β-strand	45-51	7	2
β-strand	57-59	3	2
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-96	9	2
β-strand	99-103	5	2
β-strand	107-111	5	2
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
α-helix	155-157	3
β-strand	159	1	5
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
α-helix	186-188	3
β-strand	189	1	6
β-strand	192	1	6
β-strand	195-200	6	5
α-helix	201-203	3
β-strand	205-210	6	5

Chain I: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	45-51	7	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-72	6	7
α-helix	73-75	3
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-96	9	8
β-strand	99-103	5	8
β-strand	107-111	5	8
α-helix	114-116	3
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-185	10	10
α-helix	186-188	3
β-strand	189	1	12
β-strand	192	1	12
β-strand	195-200	6	11
α-helix	201-203	3
β-strand	205-210	6	11

Chains L and M: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
α-helix	55	1
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	85-90	6	14
α-helix	96	1
β-strand	97-98	2	14
β-strand	102-106	5	14
β-strand	111	1	15
α-helix	112-113	2
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	16
β-strand	140	1	15
β-strand	145-150	6	17
β-strand	153-154	2	17
α-helix	155	1
β-strand	159-163	5	16
α-helix	164-167	4
β-strand	173-182	10	16
α-helix	183-186	4
β-strand	191-197	7	17
β-strand	205-210	6	17

Chains W and Y: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	23
β-strand	9-13	4	24
β-strand	18-25	8	23
α-helix	29-31	3
β-strand	34-39	6	24
β-strand	43-49	7	24
β-strand	53-54	2	24
α-helix	55	1
β-strand	62-67	6	23
β-strand	70-76	7	23
α-helix	80-82	3
β-strand	84-91	8	24
β-strand	96-98	3	24
β-strand	99	1	23
β-strand	102-106	5	24
β-strand	112	1	25
α-helix	113-114	2
β-strand	115-119	5	26
α-helix	120-122	3
α-helix	123-126	4
β-strand	130-140	11	26
β-strand	141	1	25
β-strand	146-151	6	27
β-strand	154-155	2	27
β-strand	160-162	3	26
α-helix	163-165	3
β-strand	166-167	2	26
β-strand	171-180	10	26
α-helix	181-186	6
β-strand	190-196	7	27
β-strand	199-205	7	27

Chain X: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	28
α-helix	7-9	3
β-strand	10-12	3	29
β-strand	18-25	8	28
α-helix	29-31	3
β-strand	33-39	7	29
β-strand	41	1	30
β-strand	43	1	30
β-strand	45-52	8	29
β-strand	56-59	4	29
α-helix	61-63	3
β-strand	67-72	6	28
β-strand	77-82	6	28
α-helix	84-86	3
β-strand	88-95	8	29
β-strand	102	1	24
β-strand	103	1	29
β-strand	107-111	5	29
α-helix	114-116	3
β-strand	117	1	31
α-helix	118-119	2
β-strand	120-124	5	32
β-strand	135-145	11	32
β-strand	146	1	31
β-strand	151-154	4	33
α-helix	155-157	3
β-strand	159	1	33
β-strand	163-165	3	32
α-helix	166-168	3
β-strand	169-171	3	32
β-strand	174-184	11	32
β-strand	194-199	6	33
α-helix	200-202	3
β-strand	204-209	6	33

Chain Z: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	39
α-helix	7-9	3
β-strand	10-12	3	40
β-strand	18-25	8	39
α-helix	29-31	3
β-strand	33-39	7	40
β-strand	41	1	41
β-strand	43	1	41
β-strand	45-52	8	40
β-strand	56-59	4	40
α-helix	61-63	3
β-strand	67-72	6	39
β-strand	77-82	6	39
α-helix	84-86	3
β-strand	88-95	8	40
β-strand	102	1	35
β-strand	103	1	40
β-strand	107-111	5	40
α-helix	114-116	3
β-strand	117	1	42
β-strand	120-124	5	43
β-strand	135-145	11	43
β-strand	146	1	42
β-strand	151-154	4	44
α-helix	155-157	3
β-strand	163-165	3	43
α-helix	166-168	3
β-strand	169-171	3	43
β-strand	174-184	11	43
β-strand	194-199	6	44
α-helix	200-202	3
β-strand	204-209	6	44

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
humanized antibody D3H44	H, I	protein	217	Mus musculus, Homo sapiens	P01857 (AlphaFold model)
humanized antibody D3H44	L, M	protein	213	Mus musculus, Homo sapiens	Q7Z3Y4 (AlphaFold model)
murine antibody 6A6 Fab fragment	W, Y	protein	210	Mus musculus	G0YP42 (AlphaFold model)
murine antibody 6A6 Fab fragment	X, Z	protein	220	Mus musculus	P01863 (AlphaFold model)

Sequence of entity 1 (H, I), FASTA

>1PG7_1 humanized antibody D3H44 (chains H, I)
EVQLVESGGGLVQPGGSLRLSCAASGFNIKEYYMHWVRQAPGKGLEWVGLIDPEQGNTIY
DPKFQDRATISADNSKNTAYLQMNSLRAEDTAVYYCARDTAAYFDYWGQGTLVTVSSAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Sequence of entity 2 (L, M), FASTA

>1PG7_2 humanized antibody D3H44 (chains L, M)
DIQMTQSPSSLSASVGDRVTITCRASRDIKSYLNWYQQKPGKAPKVLIYYATSLAEGVPS
RFSGSGSGTDYTLTISSLQPEDFATYYCLQHGESPWTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Sequence of entity 3 (W, Y), FASTA

>1PG7_3 murine antibody 6A6 Fab fragment (chains W, Y)
QAVVTQESALTSSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGVIGGTNNRAPGV
PARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLGQPKSSPSVNL
FPPSSEELKTKKATLVCTITEFYPGAVRVDWKADGTPVTQGDETTQPSKQSNNKYMASSY
LTLTAEAWESHSSYSCHVTHEGQSVEKSLS

Sequence of entity 4 (X, Z), FASTA

>1PG7_4 murine antibody 6A6 Fab fragment (chains X, Z)
EVQLQQSGPELVKPGASVKISCKASGYSFTGHLLNWVKQSHGKNLEWIGLVHPHNGAITY
NQKFKDKATLTVDRSSTTAYIELVRLTSNDSAVYYCAREDFRYHYSMDYWGQGTSVTVSS
AKTTPPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVTSSTWPSQSVTCNVAHPASSTKVDKKIVPK

Primary citation

Structural insight into how an anti-idiotypic antibody against D3H44 (anti-tissue factor antibody) restores normal coagulation. Eigenbrot, C., Meng, Y.G., Krishnamurthy, R. et al. J Mol Biol (2003) 331:433-446. DOI 10.1016/S0022-2836(03)00735-6 · PubMed

Other PDB entries of the same protein (UniProt P01857 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LLD 1.19 Å, Structure of wild-type IgG1 antibody heavy chain constant domain 1 and light chain…
3TV3 1.29 Å, Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with…
4LLQ 1.42 Å, Structure of redesigned IgG1 first constant and lambda domains (CH1:Clambda constant…
5HSF 1.52 Å, 1.52 Angstrom Crystal Structure of Fc fragment of Human IgG1.
6YT7 1.55 Å, Glycosylated knob/dummy-hole fc fragment
4NWU 1.6 Å, Crystal structure of APE1551, an anti-human NGF Fab with a nine amino acid insertion in…
1L6X 1.65 Å, Fc fragment of rituximab bound to a minimized version of the B-domain from protein A…
3TWC 1.65 Å, Crystal structure of broad and potent HIV-1 neutralizing antibody PGT127 in complex with…
5JIH 1.66 Å, Crystal structure of HER2 binding IgG1-Fc (Fcab STAB19)
3MCL 1.7 Å, Anti-beta-amyloid antibody c706 fab in space group P21
5U66 1.7 Å, Modified single helix from the B-domain of protein A bound to IgG1 Fc
6N35 1.75 Å, Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement

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