2R56: Recombinant IgE Fab Fragment

Crystal Structure of a Recombinant IgE Fab Fragment in Complex with Bovine Beta-Lactoglobulin Allergen. Determined by X-ray diffraction at 2.8 Å resolution. Released 13 Nov 2007.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Bos taurus, Homo sapiens
Chains: 6
Atoms: 9,136
Mol. weight: 130.75 kDa
Ligands: LMT
Released: 13 Nov 2007

Explore 2R56 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2R56 contains 32 α-helices and 113 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: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
β-strand	17-18	2	1
β-strand	20-26	7	1
α-helix	29-31	3
β-strand	41-48	8	1
β-strand	54-61	8	1
β-strand	66-75	10	1
β-strand	81-84	4	1
α-helix	87-89	3
β-strand	90-97	8	1
β-strand	102-109	8	1
β-strand	117-123	7	1
α-helix	130-140	11
β-strand	147-150	4	1
α-helix	153-157	5

Chain B: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
β-strand	17-18	2	1
β-strand	20-26	7	1
α-helix	29-31	3
β-strand	41-48	8	1
β-strand	54-61	8	1
β-strand	66-75	10	1
β-strand	81-84	4	1
α-helix	87-89	3
β-strand	90-97	8	1
β-strand	102-109	8	1
β-strand	117-123	7	1
α-helix	130-140	11
β-strand	147-150	4	1
α-helix	155-157	3

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	11-12	2	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	65	1	8
β-strand	68-73	6	8
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-99	8	10
β-strand	108-111	4	10
β-strand	115-117	3	10
β-strand	118-119	2	9
α-helix	123-124	2
β-strand	125	1	11
β-strand	128-132	5	12
α-helix	136-138	3
β-strand	143-153	11	12
β-strand	154	1	11
β-strand	159-162	4	13
β-strand	167	1	13
β-strand	172-173	2	12
α-helix	174-176	3
β-strand	177-178	2	12
β-strand	184-193	10	12
α-helix	194-196	3
β-strand	203-208	6	13
β-strand	213-218	6	13

Chain I: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	11-12	2	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	34-39	6	21
β-strand	45-51	7	21
β-strand	58-60	3	21
β-strand	65	1	19
β-strand	68-73	6	19
β-strand	78-83	6	19
α-helix	88-90	3
β-strand	92-99	8	21
β-strand	108-111	4	21
β-strand	115-117	3	21
β-strand	118-119	2	20
α-helix	122-124	3
β-strand	125	1	22
β-strand	128-132	5	23
β-strand	143-153	11	23
β-strand	154	1	22
β-strand	159-162	4	24
β-strand	167	1	24
β-strand	172-173	2	23
α-helix	174-176	3
β-strand	177-178	2	23
β-strand	184-193	10	23
α-helix	194-196	3
β-strand	203-208	6	24
β-strand	213-218	6	24

Chain L: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	2
β-strand	10-14	5	3
β-strand	15	1	4
β-strand	17	1	4
β-strand	19-25	7	2
β-strand	33-38	6	3
β-strand	45-49	5	3
β-strand	53-54	2	3
α-helix	55	1
β-strand	62-67	6	2
β-strand	70-75	6	2
β-strand	84-90	7	3
α-helix	96	1
β-strand	97-98	2	3
β-strand	99	1	2
β-strand	102-107	6	3
β-strand	111	1	5
β-strand	114-118	5	6
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	6
β-strand	140	1	5
β-strand	145-150	6	7
β-strand	153	1	7
β-strand	159-163	5	6
β-strand	173-182	10	6
α-helix	183-188	6
β-strand	191-197	7	7
β-strand	205-210	6	7

Chain M: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	14
β-strand	10-14	5	15
β-strand	19-25	7	14
β-strand	33-38	6	15
β-strand	45-49	5	15
β-strand	53-54	2	15
β-strand	62-67	6	14
β-strand	70-75	6	14
β-strand	84-90	7	15
α-helix	96	1
β-strand	97-98	2	15
β-strand	99	1	14
β-strand	102-107	6	15
β-strand	111	1	16
β-strand	114-118	5	17
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	17
β-strand	140	1	16
β-strand	144-150	7	18
β-strand	159-163	5	17
β-strand	173-182	10	17
α-helix	183-188	6
β-strand	191-198	8	18
β-strand	205-210	6	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-lactoglobulin	A, B	protein	162	Bos taurus	P02754 (AlphaFold model)
IgE Fab Fragment, light chain	L, M	protein	211	Homo sapiens	P0DOX7 (AlphaFold model)
IgE Fab Fragment, heavy chain	H, I	protein	221	Homo sapiens	P01857 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2R56_1 Beta-lactoglobulin (chains A, B)
LIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSAPLRVYVEELKPTPEGDLEILLQK
WENGECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQ
CLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI

Sequence of entity 2 (L, M), FASTA

>2R56_2 IgE Fab Fragment, light chain (chains L, M)
DIVMTQSPSSLSASVGDRVTITCRASQGISSRLAWYQQKPGKAPKLLIYAASSLQSGVPS
RFSGSGSGTEFTLTISSLQPEDFATYYCQQYHSYPWTFGQGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Sequence of entity 3 (H, I), FASTA

>2R56_3 IgE Fab Fragment, heavy chain (chains H, I)
QVSLRESGGGLVQPGRSLRLSCTASGFTFRHHGMTWVRQAPGKGLEWVASLSGSGTKTHF
ADSVKGRFTISRDNSNNTLYLQMDNVRDEDTAIYYCAKAKRVGATGYFDLWGRGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEP

Ligands and cofactors

ID	Name	Formula	Copies
LMT	Dodecyl-beta-D-maltoside	C24 H46 O11	2

Primary citation

Molecular interactions between a recombinant IgE antibody and the beta-lactoglobulin allergen. Niemi, M., Jylha, S., Laukkanen, M.L. et al. Structure (2007) 15:1413-1421. DOI 10.1016/j.str.2007.09.012 · PubMed

Other PDB entries of the same protein (UniProt P02754 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Q19 1.55 Å, Beta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with desipramine (FAW-DSM#3)
4GNY 1.64 Å, Bovine beta-lactoglobulin complex with dodecyl sulfate
7Q2P 1.69 Å, Beta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with desipramine (FAW-DSM#2)
5NUK 1.7 Å, Engineered beta-lactoglobulin: variant I56F-L39A-M107F in complex with chlorpromazine…
7Q2N 1.7 Å, Beta-lactoglobulin mutant FAF (I56F/L39A/M107F) in complex with desipramine (FAF-DSM)
7KOT 1.74 Å, Energetic and structural effects of the Tanford transition on the ligand recognition of…
1BEB 1.8 Å, Bovine beta-lactoglobulin, lattice X
7BF8 1.8 Å, Mutant I56F of recombinant bovine beta-lactoglobulin in complex with tetracaine
7BF9 1.8 Å, Mutant M107L of recombinant bovine beta-lactoglobulin in complex with tetracaine
7Q17 1.8 Å, Beta-lactoglobulin mutant FAW (I56F/L39A/M107W), unliganded form
7Q2O 1.8 Å, Beta-lactoglobulin mutant FAW (I56F/L39A/M107W) in complex with desipramine (FAW-DSM#1)
7Q18 1.8 Å, Beta-lactoglobulin mutant FAF (I56F/L39A/M107F), unliganded form

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