1YEE: Catalytic antibody, IGG2A FAB fragment

Name: PDB 1YEE: Structure of a catalytic antibody, IGG2A FAB fragment (D2.5)
Published: 1997-10-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: catalytic antibody

Structure of a catalytic antibody, IGG2A FAB fragment (D2.5). Determined by X-ray diffraction at 2.2 Å resolution. Released 15 Oct 1997.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,495
Mol. weight: 48.39 kDa
Ligands: PNB
Released: 15 Oct 1997

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

Secondary structure: helices and β-sheets

1YEE contains 16 α-helices and 47 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, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-40	7	8
β-strand	44-52	9	8
β-strand	56-59	4	8
α-helix	61-63	3
β-strand	64	1	7
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-94	7	8
β-strand	97-98	2	9
β-strand	100C-100D	2	9
β-strand	102-103	2	8
β-strand	107-111	5	8
α-helix	114-116	3
β-strand	117	1	10
β-strand	120-124	5	11
β-strand	135-145	11	11
β-strand	146	1	10
β-strand	151-155	4	12
α-helix	160-162	3
β-strand	164	1	12
β-strand	169-177	9	11
β-strand	182-192	11	11
β-strand	204-210	6	12
α-helix	211-213	3
β-strand	215-220	6	12

Chain L: 9 helices, 23 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	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	102-106	5	2
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-125	4
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	183-186	4
β-strand	191-197	7	6
α-helix	204	1
β-strand	205-210	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IGG2A FAB fragment (D2.5)	L	protein	219	Mus musculus
IGG2A FAB fragment (D2.5)	H	protein	222	Mus musculus	P01865 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1YEE_1 IGG2A FAB FRAGMENT (D2.5) (chains L)
DIVMTQSPLTLSVTIGQPASISCKSSQSLLYSNGKTYLSWLLQRPGQSPKRLIYLVSKLD
SGVPDRFTGSGSGTDFTLKISRVEAADLGLYYCVQGTHFPYTFGGGTKLEILRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>1YEE_2 IGG2A FAB FRAGMENT (D2.5) (chains H)
EVKLQESGAELVRPGASVKLSCKTSGYIFTSYWIHWVKQRAAAGLEWIARIYPGTGSSYY
NVKFKGKATLTADKSSSTAYMQLSSLKSDDSAVYFCVRWGFIPVREDYVLDYWGQGTLVT
VSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVL
QSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP

Ligands and cofactors

ID	Name	Formula	Copies
PNB	4-nitro-benzylphosphonobutanoyl-glycine	C13 H17 N2 O8 P	1

Primary citation

Structural convergence in the active sites of a family of catalytic antibodies. Charbonnier, J.B., Golinelli-Pimpaneau, B., Gigant, B. et al. Science (1997) 275:1140-1142. DOI 10.1126/science.275.5303.1140 · PubMed

Other PDB entries of the same protein (UniProt P01865 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1NCW 1.3 Å, Cationic Cyclization Antibody 4C6 in Complex with Benzoic Acid
1RUK 1.4 Å, Crystal structure (C) of native cationic cyclization antibody 4C6 fab at pH 4.6 with a…
1RUP 1.4 Å, Crystal structure (G) of native cationic cyclization antibody 4C6 fab at pH 8.5 with a…
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…
1NBY 1.8 Å, Crystal Structure of HyHEL-63 complexed with HEL mutant K96A
1FLR 1.85 Å, 4-4-20 FAB fragment
6UQC 1.87 Å, Mouse IgG2a Bispecific Fc
1RUL 1.88 Å, Crystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6…
1NDG 1.9 Å, Crystal structure of Fab fragment of antibody HyHEL-8 complexed with its antigen lysozyme
2ADF 1.9 Å, Crystal Structure and Paratope Determination of 82D6A3, an Antithrombotic Antibody…
3FO9 1.9 Å, Crystal structure of aldolase antibody 33F12 Fab' in complex with hapten 1,3-diketone

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