1ND0: Immunoglobulin IGG2A

Cationic cyclization antibody 4C6 complex with transition state analog. Determined by X-ray diffraction at 2.45 Å resolution. Released 13 May 2003.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Mus musculus
Chains: 8
Atoms: 14,002
Mol. weight: 193.52 kDa
Ligands: DP4
Released: 13 May 2003

Explore 1ND0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1ND0 contains 54 α-helices and 181 β-strands across 8 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.

Chains A, C, E and G: 7 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
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	97-98	2	2
β-strand	102-107	6	2
β-strand	111	1	4
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-155	3	6
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-187	5
β-strand	191-198	8	6
β-strand	201-210	10	6

Chains B and D: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
β-strand	33-39	8	9
β-strand	45-52	8	9
β-strand	57-59	3	9
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	9
β-strand	102-103	2	9
β-strand	107-109	3	9
β-strand	110-111	2	8
α-helix	115-116	2
β-strand	117	1	10
β-strand	120-124	5	11
β-strand	137-147	11	11
β-strand	148	1	10
β-strand	153-157	4	12
α-helix	162-164	3
β-strand	171-173	3	11
α-helix	174-176	3
β-strand	177-179	3	11
β-strand	184-194	11	11
β-strand	206-212	6	12
α-helix	213-215	3
β-strand	217-222	6	12

Chain F: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	31
β-strand	11-12	2	32
β-strand	18-25	8	31
β-strand	33-39	8	26
β-strand	45-52	8	26
β-strand	57-59	3	26
α-helix	61-63	3
β-strand	67-68	2	31
β-strand	71-72	2	31
β-strand	77-82	6	31
α-helix	84-86	3
β-strand	88-96	9	26
β-strand	102-103	2	26
β-strand	107-109	3	26
β-strand	110-111	2	32
α-helix	115-116	2
β-strand	117	1	33
β-strand	120-124	5	34
β-strand	137-147	11	34
β-strand	148	1	33
β-strand	153-157	4	35
α-helix	162-164	3
β-strand	171-173	3	34
α-helix	174-176	3
β-strand	177-179	3	34
β-strand	184-194	11	34
β-strand	206-212	6	35
α-helix	213-215	3
β-strand	217-222	6	35
α-helix	226-227	2

Chain H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	42
β-strand	11-12	2	43
β-strand	18-25	8	42
β-strand	33-39	8	44
β-strand	45-52	8	44
β-strand	57-59	3	44
α-helix	61-63	3
β-strand	67-72	6	42
β-strand	77-82	6	42
α-helix	84-86	3
β-strand	88-96	9	44
β-strand	102-103	2	44
β-strand	107-109	3	44
β-strand	110-111	2	43
α-helix	115-116	2
β-strand	117	1	45
β-strand	120-124	5	46
β-strand	137-147	11	46
β-strand	148	1	45
β-strand	153-157	4	47
α-helix	162-164	3
β-strand	171-173	3	46
α-helix	174-176	3
β-strand	177-179	3	46
β-strand	184-194	11	46
β-strand	206-212	6	47
α-helix	213-215	3
β-strand	217-222	6	47
α-helix	226-227	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin IGG2A	A, C, E, G	protein	219	Mus musculus	Q58EU8 (AlphaFold model)
Immunoglobulin IGG2A	B, D, F, H	protein	222	Mus musculus	P01865 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>1ND0_1 IMMUNOGLOBULIN IGG2A (chains A, C, E, G)
DVVMTQSPKTISVTIGQPASISCKSSQRLLNSNGKTFLNWLLQRPGQSPKRLIYLGTKLD
SGVPDRFTGSGSGTDFTLKISRVEAEDLGVYYCWQGTHFPYTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B, D, F, H), FASTA

>1ND0_2 IMMUNOGLOBULIN IGG2A (chains B, D, F, H)
RVQLQQSGPGLVKPSQSLSLTCTVTGYSITSDFAWNWIRQFPGNKLEWMGYINYSGFTSH
NPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCAGLLWYDGGAGSWGQGTLVTVSAA
KTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPT

Ligands and cofactors

ID	Name	Formula	Copies
DP4	(1s,4s)-4-[dimethyl(phenyl)silyl]-1-methylpiperidine 1-oxide	C14 H23 N O Si	4

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

Primary citation

Structural Basis for Antibody Catalysis of a Cationic Cyclization Reaction. Zhu, X., Heine, A., Monnat, F. et al. J Mol Biol (2003) 329:69-83. DOI 10.1016/S0022-2836(03)00406-6 · PubMed

Other PDB entries of the same protein (UniProt Q58EU8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1NCW 1.3 Å, Cationic Cyclization Antibody 4C6 in Complex with Benzoic Acid
9H8H 1.33 Å, Structure of DC11 anti tau antibody Fab fragment
1RUM 1.48 Å, Crystal structure (F) of H2O2-soaked cationic cyclization antibody 4C6 fab at pH 8.5…
1RUA 1.75 Å, Crystal structure (B) of u.v.-irradiated cationic cyclization antibody 4C6 fab at pH 4.6…
1YEJ 1.85 Å, Catalytic antibody complex
1KN2 1.9 Å, Catalytic antibody D2.3 complex
1KN4 1.9 Å, Catalytic antibody D2.3 complex
1YEI 1.9 Å, Catalytic antibody D2.3 complex
2C1P 2.0 Å, Fab-fragment of enantioselective antibody complexed with finrozole
1YEK 2.1 Å, Catalytic antibody D2.3 complex
2C1O 2.75 Å, ENAIIHis Fab fragment in the free form

Browse structure collections

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