2O5Z: Chimeric antibody Fab 1E9-DB3

Crystal structure of the 1E9 LeuH47Trp/ArgH100Trp Fab 5-beta-androstane-3,17-dione complex. Determined by X-ray diffraction at 2.4 Å resolution. Released 18 Dec 2007.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Mus musculus, Homo sapiens
Chains: 2
Atoms: 3,735
Mol. weight: 51.07 kDa
Ligands: ANO
Released: 18 Dec 2007

Explore 2O5Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2O5Z contains 18 α-helices and 45 β-strands across 2 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: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	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
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-96	9	8
β-strand	100A-103	5	8
β-strand	107-111	5	8
α-helix	115-116	2
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
β-strand	137-147	11	10
β-strand	148	1	9
β-strand	153-157	4	11
α-helix	162-164	3
β-strand	166	1	11
β-strand	171-173	3	10
α-helix	174-176	3
β-strand	177-178	2	10
β-strand	185-194	10	10
α-helix	195-202	5
β-strand	206-212	7	11
α-helix	213-215	3
β-strand	217-223	7	11

Chain L: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	27C	1	3
β-strand	31	1	3
β-strand	33-38	6	2
α-helix	43-44	2
β-strand	45-49	5	2
β-strand	53-54	2	2
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	97-98	2	2
β-strand	102-107	6	2
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-154	2	6
α-helix	155	1
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-186	4
β-strand	191-197	7	6
β-strand	205-210	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
chimeric antibody Fab 1E9-DB3	L	protein	219	Mus musculus, Homo sapiens	P01631 (AlphaFold model), P01834 (AlphaFold model)
chimeric antibody Fab 1E9-DB3	H	protein	227	Mus musculus, Homo sapiens	P01857 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>2O5Z_1 chimeric antibody Fab 1E9-DB3 (chains L)
ELVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKFLIYKVSNRF
SGVPDRFSGSGSGTDFILKISRVEAEDLGVYFCFQSTHFFPTFGGGTKLEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (H), FASTA

>2O5Z_2 chimeric antibody Fab 1E9-DB3 (chains H)
QVQLVQSGPELKKPGETVKISCKASGYMFTNYGMNWVKQAPGKALKWMGWINPYTGESTF
ADDFKGRFAFFLETSATTAYLQINNLKNEDTATYFCARGTTIVWAMDYWGQGTSVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPLSCDKTHT

Ligands and cofactors

ID	Name	Formula	Copies
ANO	5-beta-androstane-3,17-dione	C19 H28 O2	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Closely related antibody receptors exploit fundamentally different strategies for steroid recognition. Verdino, P., Aldag, C., Hilvert, D. et al. Proc Natl Acad Sci U S A (2008) 105:11725-11730. DOI 10.1073/pnas.0801783105 · PubMed

Other PDB entries of the same protein (UniProt P01631 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1DLF 1.45 Å, High resolution crystal structure of the fv fragment from an anti-dansyl switch variant…
2DLF 1.55 Å, High resolution crystal structure of the fv fragment from an anti-dansyl switch variant…
1N4X 1.7 Å, Structure of scFv 1696 at acidic pH
1WZ1 1.85 Å, Crystal structure of the Fv fragment complexed with dansyl-lysine
1SVZ 1.89 Å, Crystal structure of the single-chain Fv fragment 1696 in complex with the epitope…
2IPT 2.0 Å, PFA1 Fab Fragment
2IQA 2.0 Å, PFA2 FAB fragment, monoclinic apo form
2HKF 2.01 Å, Crystal structure of the Complex Fab M75- Peptide
2O5X 2.05 Å, Crystal structure of 1E9 LeuH47Trp/ArgH100Trp, an engineered Diels-Alderase Fab with nM…
1BFV 2.1 Å, Monoclonal antibody fragment FV4155 from E. Coli
1CFV 2.1 Å, Monoclonal antibody fragment FV4155 from E. Coli
2HKH 2.1 Å, Crystal structure of the Fab M75

Browse structure collections

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