25C8: Catalytic antibody 5C8, FAB-hapten complex

Name: PDB 25C8: Catalytic antibody 5C8, FAB-hapten complex
Published: 1999-03-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: catalytic antibody

Catalytic antibody 5C8, FAB-hapten complex. Determined by X-ray diffraction at 2.0 Å resolution. Released 23 Mar 1999.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,507
Mol. weight: 46.58 kDa
Ligands: GEP
Released: 23 Mar 1999

Explore 25C8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

25C8 contains 15 α-helices and 43 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: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
α-helix	7-9	3
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	45-52	8	7
β-strand	56-59	4	7
α-helix	61-63	3
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-94	7	7
β-strand	102-103	2	7
β-strand	107-111	5	7
α-helix	114-116	3
β-strand	117	1	8
α-helix	118-119	2
β-strand	120-124	5	9
β-strand	137-147	11	9
β-strand	148	1	8
β-strand	153-157	4	10
β-strand	166	1	10
β-strand	171-173	3	9
α-helix	174-176	3
β-strand	177-178	2	9
β-strand	185-194	10	9
β-strand	205-212	7	10
β-strand	217-223	7	10

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
α-helix	30-32	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	102-106	5	2
β-strand	111	1	3
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	144-150	7	5
β-strand	153-155	3	5
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-187	5
β-strand	191-198	8	5
β-strand	205-210	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IgG 5C8	L	protein	212	Mus musculus	P01837 (AlphaFold model)
IgG 5C8	H	protein	217	Mus musculus	P01869 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>25C8_1 IGG 5C8 (chains L)
DIVLTQSPAIMSASLGERVTMTCTASSSVSSSNLHWYQQKPGSSPKLWIYSTSNLASGVP
ARFSGSGSGTSYSLTISSMEAEDAATYYCHQYHRSPYTFGGGTKLEIKRADAAPTVSIFP
PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTL
TLTKDEYERHNSYTCEATHKTSTSPIVKSFNR

Sequence of entity 2 (H), FASTA

>25C8_2 IGG 5C8 (chains H)
EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQKPEQGLEWIAQIDPANGNTKY
DPKFQGKATITADTSSNTAYLHLSSLTSEDSAVYYCAADPPYYGHGDYWGQGTTLTVSSA
KTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIV

Ligands and cofactors

ID	Name	Formula	Copies
GEP	N-methyl-N-(para-glutaramidophenyl-ethyl)-piperidinium ion	C19 H29 N2 O3	1

Primary citation

Structural basis for antibody catalysis of a disfavored ring closure reaction. Gruber, K., Zhou, B., Houk, K.N. et al. Biochemistry (1999) 38:7062-7074. DOI 10.1021/bi990210s · PubMed

Other PDB entries of the same protein (UniProt P01837 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3D9A 1.2 Å, High Resolution Crystal Structure Structure of HyHel10 Fab Complexed to Hen Egg Lysozyme
1RUR 1.5 Å, Crystal Structure (I) of native Diels-Alder antibody 13G5 Fab at pH 8.0 with a data set…
2AJU 1.5 Å, Cyrstal structure of cocaine catalytic antibody 7A1 Fab'
2AJV 1.5 Å, Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Complex with Cocaine
2W60 1.5 Å, Anti citrullinated Collagen type 2 antibody acc4
2W9D 1.57 Å, Structure of Fab fragment of the ICSM 18 - anti-Prp therapeutic antibody at 1.57 A…
3BKJ 1.59 Å, Crystal structure of Fab wo2 bound to the n terminal domain of amyloid beta peptide (1-16)
3BAE 1.59 Å, Crystal structure of Fab WO2 bound to the N terminal domain of Amyloid beta peptide (1-28)
2R1Y 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
2R2B 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
3BKM 1.6 Å, Structure of anti-amyloid-beta Fab WO2 (Form A, P212121)
3CFB 1.6 Å, High-resolution structure of blue fluorescent antibody EP2-19G2 in complex with stilbene…

Browse structure collections

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