1VFB: IgG1-kappa D1.3 fv

Bound water molecules and conformational stabilization help mediate an antigen-antibody association. Determined by X-ray diffraction at 1.8 Å resolution. Released 31 May 1994.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Mus musculus, Gallus gallus
Chains: 3
Atoms: 2,779
Mol. weight: 38.89 kDa
Released: 31 May 1994

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

Secondary structure: helices and β-sheets

1VFB contains 12 α-helices and 32 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 A: 2 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
β-strand	98	1	2
β-strand	102-106	5	2

Chain B: 2 helices, 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
α-helix	64-66	3
β-strand	67-72	6	3
β-strand	77-82	6	3
α-helix	87-89	3
β-strand	91-98	8	5
β-strand	103-106	4	5
β-strand	110-112	3	5
β-strand	113-114	2	4

Chain C: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	6
α-helix	5-14	10
β-strand	20	1	7
β-strand	23	1	7
α-helix	25-36	12
β-strand	39	1	6
β-strand	43-46	4	8
β-strand	48-53	6	8
β-strand	58-59	2	8
β-strand	65	1	9
β-strand	79	1	9
α-helix	80-84	5
α-helix	89-98	10
α-helix	104-107	4
α-helix	109-110	2
α-helix	111-115	5
α-helix	120-123	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IgG1-kappa D1.3 fv (light chain)	A	protein	107	Mus musculus	P01635 (AlphaFold model)
IgG1-kappa D1.3 fv (heavy chain)	B	protein	116	Mus musculus	P01820 (AlphaFold model)
Hen egg white lysozyme	C	protein	129	Gallus gallus	P00698 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1VFB_1 IGG1-KAPPA D1.3 FV (LIGHT CHAIN) (chains A)
DIVLTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYYTTTLADGVPS
RFSGSGSGTQYSLKINSLQPEDFGSYYCQHFWSTPRTFGGGTKLEIK

Sequence of entity 2 (B), FASTA

>1VFB_2 IGG1-KAPPA D1.3 FV (HEAVY CHAIN) (chains B)
QVQLQESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGNTDYN
SALKSRLSISKDNSKSQVFLKMNSLHTDDTARYYCARERDYRLDYWGQGTTLTVSS

Sequence of entity 3 (C), FASTA

>1VFB_3 HEN EGG WHITE LYSOZYME (chains C)
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
QAWIRGCRL

Primary citation

Bound water molecules and conformational stabilization help mediate an antigen-antibody association. Bhat, T.N., Bentley, G.A., Boulot, G. et al. Proc Natl Acad Sci U S A (1994) 91:1089-1093. DOI 10.1073/pnas.91.3.1089 · 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…
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…
1DVF 1.9 Å, Idiotopic antibody D1.3 fv fragment-antiidiotopic antibody E5.2 fv fragment complex
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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