1FDL: IgG1-kappa D1.3 FAB

Crystallographic refinement of the three-dimensional structure of the FAB D1.3-lysozyme complex at 2.5-Å resolution. Determined by X-ray diffraction at 2.5 Å resolution. Released 15 Oct 1991.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Mus musculus, Gallus gallus
Chains: 3
Atoms: 4,309
Mol. weight: 61.41 kDa
Released: 15 Oct 1991

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

Secondary structure: helices and β-sheets

1FDL contains 18 α-helices and 52 β-strands across 3 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: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	46-51	6	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	68-72	5	6
β-strand	77-82	6	6
β-strand	91-98	8	8
β-strand	103-106	4	8
β-strand	110-112	3	8
β-strand	113-114	2	7
β-strand	120	1	9
β-strand	123-127	5	10
β-strand	138-148	11	10
β-strand	149	1	9
β-strand	154-157	4	11
α-helix	158-160	3
β-strand	162	1	11
β-strand	167-173	7	10
β-strand	178-187	10	10
β-strand	197-202	6	11
α-helix	203-205	3
β-strand	207-212	6	11

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	98	1	2
β-strand	102-106	5	2
β-strand	111	1	3
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-155	3	5
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	191-197	7	5
β-strand	205-210	6	5

Chain Y: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	12
α-helix	5-14	10
β-strand	20	1	13
β-strand	23	1	13
α-helix	26-36	11
β-strand	39	1	12
β-strand	43-46	4	14
β-strand	50-53	4	14
β-strand	58-59	2	14
β-strand	65	1	15
β-strand	79	1	15
α-helix	80-84	5
α-helix	89-100	12
α-helix	104-107	4
α-helix	111-114	4
α-helix	120-124	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IgG1-kappa D1.3 FAB (light chain)	L	protein	214	Mus musculus	P01837 (AlphaFold model)
IgG1-kappa D1.3 FAB (heavy chain)	H	protein	218	Mus musculus	P01868 (AlphaFold model)
Hen egg white lysozyme	Y	protein	129	Gallus gallus	P00698 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1FDL_1 IGG1-KAPPA D1.3 FAB (LIGHT CHAIN) (chains L)
DIQMTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYYTTTLADGVPS
RFSGSGSGTQYSLKINSLQPEDFGSYYCQHFWSTPRTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>1FDL_2 IGG1-KAPPA D1.3 FAB (HEAVY CHAIN) (chains H)
QVQLKESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGNTDYN
SALKSRLSISKDNSKSQVFLKMNSLHTDDTARYYCARERDYRLDYWGQGTTLTVSSASTT
PPSVFPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTL
SSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 3 (Y), FASTA

>1FDL_3 HEN EGG WHITE LYSOZYME (chains Y)
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
QAWIRGCRL

Primary citation

Crystallographic refinement of the three-dimensional structure of the FabD1.3-lysozyme complex at 2.5-A resolution. Fischmann, T.O., Bentley, G.A., Bhat, T.N. et al. J Biol Chem (1991) 266:12915-12920. PubMed

Other PDB entries of the same protein (UniProt P01837 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3D9A 1.2 Å, High Resolution Crystal Structure Structure of HyHel10 Fab Complexed to Hen Egg Lysozyme
1RUR 1.5 Å, Crystal Structure (I) of native Diels-Alder antibody 13G5 Fab at pH 8.0 with a data set…
2AJU 1.5 Å, Cyrstal structure of cocaine catalytic antibody 7A1 Fab'
2AJV 1.5 Å, Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Complex with Cocaine
2W60 1.5 Å, Anti citrullinated Collagen type 2 antibody acc4
2W9D 1.57 Å, Structure of Fab fragment of the ICSM 18 - anti-Prp therapeutic antibody at 1.57 A…
3BKJ 1.59 Å, Crystal structure of Fab wo2 bound to the n terminal domain of amyloid beta peptide (1-16)
3BAE 1.59 Å, Crystal structure of Fab WO2 bound to the N terminal domain of Amyloid beta peptide (1-28)
2R1Y 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
2R2B 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
3BKM 1.6 Å, Structure of anti-amyloid-beta Fab WO2 (Form A, P212121)
3CFB 1.6 Å, High-resolution structure of blue fluorescent antibody EP2-19G2 in complex with stilbene…

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1FDL is part of these collections:

Antibodies and the immune system

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