1DVF: FV D1.3

Idiotopic antibody D1.3 fv fragment-antiidiotopic antibody E5.2 fv fragment complex. Determined by X-ray diffraction at 1.9 Å resolution. Released 17 Aug 1996.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Mus musculus
Chains: 4
Atoms: 3,654
Mol. weight: 50 kDa
Ligands: ZN
Released: 17 Aug 1996

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

Secondary structure: helices and β-sheets

1DVF contains 11 α-helices and 47 β-strands across 4 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: 3 helices, 11 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

Chain B: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	3
β-strand	11-12	2	4
β-strand	18-25	8	3
β-strand	33-39	7	5
β-strand	46-51	6	5
β-strand	57-59	3	5
β-strand	67-72	6	3
β-strand	77-82	6	3
α-helix	87-89	3
β-strand	91-99	9	5
β-strand	102-106	5	5
β-strand	110-112	3	5
β-strand	113-114	2	4

Chain C: 3 helices, 11 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	33-38	6	7
β-strand	44-49	6	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-90	6	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-106	5	7

Chain D: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	8
β-strand	11-12	2	9
β-strand	17-25	9	8
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	45-51	7	7
β-strand	57-59	3	7
α-helix	61-63	3
β-strand	64	1	8
β-strand	67-72	6	8
α-helix	73-75	3
β-strand	77-82A	7	8
α-helix	84-86	3
β-strand	88-94	7	7
β-strand	102-103	2	7
β-strand	107-109	3	7
β-strand	110-111	2	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
FV D1.3	A	protein	108	Mus musculus	P01635 (AlphaFold model)
FV D1.3	B	protein	116	Mus musculus	P01820 (AlphaFold model)
FV E5.2	C	protein	107	Mus musculus	P01646 (AlphaFold model)
FV E5.2	D	protein	121	Mus musculus	A0NA69 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1DVF_1 FV D1.3 (chains A)
DIVLTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYYTTTLADGVPS
RFSGSGSGTQYSLKINSLQPEDFGSYYCQHFWSTPRTFGGGTKLEIKR

Sequence of entity 2 (B), FASTA

>1DVF_2 FV D1.3 (chains B)
QVQLQESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGNTDYN
SALKSRLSISKDNSKSQVFLKMNSLHTDDTARYYCARERDYRLDYWGQGTTLTVSS

Sequence of entity 3 (C), FASTA

>1DVF_3 FV E5.2 (chains C)
DIQLTQSPSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPS
RFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPWTFGGGTKLEIK

Sequence of entity 4 (D), FASTA

>1DVF_4 FV E5.2 (chains D)
QVQLQQSGTELVKSGASVKLSCTASGFNIKDTHMNWVKQRPEQGLEWIGRIDPANGNIQY
DPKFRGKATITADTSSNTAYLQLSSLTSEDTAVYYCATKVIYYQGRGAMDYWGQGTTLTV
S

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Primary citation

Crystal structure of an Fv-Fv idiotope-anti-idiotope complex at 1.9 A resolution. Braden, B.C., Fields, B.A., Ysern, X. et al. J Mol Biol (1996) 264:137-151. DOI 10.1006/jmbi.1996.0629 · PubMed

Other PDB entries of the same protein (UniProt P01635 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1A2Y 1.5 Å, Hen egg white lysozyme, D18A mutant, in complex with mouse monoclonal antibody D1.3
1VFA 1.8 Å, Bound water molecules and conformational stabilization help mediate an antigen-antibody…
1VFB 1.8 Å, Bound water molecules and conformational stabilization help mediate an antigen-antibody…
1WEJ 1.8 Å, IgG1 FAB fragment (of E8 antibody) complexed with horse cytochrome C at 1.8 a resolution
1KIQ 1.85 Å, Fv mutant y(b 101)F (vh domain) of mouse monoclonal antibody D1.3 complexed with hen egg…
1A7O 2.0 Å, Fv fragment of mouse monoclonal antibody D1.3 (balb/c, IgG1, K) R96L deletion mutant on…
1A7Q 2.0 Å, Fv fragment of mouse monoclonal antibody D1.3 (balb/c, IgG1, K) high affinity expressed…
1A7N 2.01 Å, Fv fragment of mouse monoclonal antibody D1.3 (balb/c, IgG1, K) variant for chain L…
1A7P 2.01 Å, Fv fragment of mouse monoclonal antibody D1.3 (balb/c, IgG1, K) engineered mutant…
1A7R 2.01 Å, Fv fragment of mouse monoclonal antibody D1.3 (balb/c, IgG1, K) variant chain L GLU81->asp
1KIP 2.1 Å, Fv mutant y(b 32)A (vh domain) of mouse monoclonal antibody D1.3 complexed with hen egg…
1QBL 2.26 Å, FAB E8 (FABE8A) X-ray structure at 2.26 Å resolution

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