1RUP: Immunoglobulin igg2a, heavy chain

Crystal structure (G) of native cationic cyclization antibody 4C6 fab at pH 8.5 with a data set collected at APS beamline 19-ID. Determined by X-ray diffraction at 1.4 Å resolution. Released 2 Mar 2004.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,902
Mol. weight: 48.53 kDa
Ligands: BEZ
Released: 2 Mar 2004

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

Secondary structure: helices and β-sheets

1RUP contains 18 α-helices and 46 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: 11 helices, 23 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	33-40	9	9
β-strand	44-52	9	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	114-116	3
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
α-helix	125-127	3
α-helix	128-130	3
β-strand	137-147	11	11
β-strand	148	1	10
β-strand	153-157	4	12
α-helix	162-164	3
β-strand	166	1	12
β-strand	171-173	3	11
α-helix	174-176	3
β-strand	177-179	3	11
β-strand	184-194	11	11
α-helix	195-198	3
β-strand	206-212	6	12
α-helix	213-215	3
β-strand	217-222	6	12
α-helix	226-227	2

Chain L: 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	44-49	6	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	122-126	5
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-154	2	6
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-188	6
β-strand	191-198	8	6
β-strand	201-210	10	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
immunoglobulin igg2a, heavy chain	L	protein	219	Mus musculus	Q8K0F8
immunoglobulin igg2a, light chain	H	protein	222	Mus musculus	P01865 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1RUP_1 immunoglobulin igg2a, heavy chain (chains L)
DVVMTQSPKTISVTIGQPASISCKSSQRLLNSNGKTFLNWLLQRPGQSPKRLIYLGTKLD
SGVPDRFTGSGSGTDFTLKISRVEAEDLGVYYCWQGTHFPYTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>1RUP_2 immunoglobulin igg2a, light chain (chains H)
RVQLQQSGPGLVKPSQSLSLTCTVTGYSITSDFAWNWIRQFPGNKLEWMGYINYSGFTSH
NPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCAGLLWYDGGAGSWGQGTLVTVSAA
KTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPT

Ligands and cofactors

ID	Name	Formula	Copies
BEZ	Benzoic acid	C7 H6 O2	1

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

Primary citation

Probing the antibody-catalyzed water-oxidation pathway at atomic resolution. Zhu, X., Wentworth Jr., P., Wentworth, A.D. et al. Proc Natl Acad Sci U S A (2004) 110:2247-2252. DOI 10.1073/pnas.0307311101 · PubMed

Other PDB entries of the same protein (UniProt Q8K0F8), best resolution first:

1RUK 1.4 Å, Crystal structure (C) of native cationic cyclization antibody 4C6 fab at pH 4.6 with a…
1RUL 1.88 Å, Crystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6…
1RU9 2.5 Å, Crystal Structure (A) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 4.6…

Browse structure collections

About this viewer

MolViewer shows 1RUP directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.