1YEC: Catalytic antibody IGG2A FAB fragment

Name: PDB 1YEC: Structure of a catalytic antibody IGG2A FAB fragment (D2.3)
Published: 1997-10-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: catalytic antibody

Structure of a catalytic antibody IGG2A FAB fragment (D2.3). Determined by X-ray diffraction at 1.9 Å resolution. Released 15 Oct 1997.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,568
Mol. weight: 49.01 kDa
Ligands: ZN, PNB
Released: 15 Oct 1997

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

Secondary structure: helices and β-sheets

1YEC contains 14 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: 8 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	34-39	6	8
β-strand	45-52	8	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	169-171	3	11
α-helix	172-174	3
β-strand	175-177	3	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: 6 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
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	144-150	7	6
β-strand	153-155	3	6
β-strand	159-163	5	5
β-strand	173-182	10	5
α-helix	183-186	4
β-strand	191-198	8	6
β-strand	205-210	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IGG2A FAB fragment (D2.3)	L	protein	219	Mus musculus
IGG2A FAB fragment (D2.3)	H	protein	222	Mus musculus	P01863 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1YEC_1 IGG2A FAB FRAGMENT (D2.3) (chains L)
DIVMTQSPLTLSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIHLVSKLD
SGVPDRITGSGSGTDFTLKISRVEAADLGVYYCVQGTHFPYTFGGGTKLEILRGDAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>1YEC_2 IGG2A FAB FRAGMENT (D2.3) (chains H)
EMQLQQSGAELLRPGTSVKLSCKTSGYIFTSYWIHWVKQRSGQGLEWIARIYPGTGSTYY
NEKFKGKATLTADKSSSTAYMQLSTLKSEDSAVYFCTRWGFIPVREDYVMDYWGQGTLVT
VSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVL
QSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7
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 P01863 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VAA 1.55 Å, Crystal structure of mouse IgG2a Fc T370K mutant
3OZ9 1.6 Å, Crystal Structure of anti-gp41 Fab NC-1
2IPU 1.65 Å, PFA1 Fab fragment complexed with Abeta 1-8 peptide
1DQQ 1.8 Å, Crystal structure of anti-lysozyme antibody hyhel-63
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
1UYW 2.0 Å, Crystal Structure of the antiflavivirus Fab4g2
1YEF 2.0 Å, Structure of IGG2A FAB fragment (D2.3) complexed with substrate analogue
1YEG 2.0 Å, Structure of IGG2A FAB fragment (D2.3) complexed with reaction product
1FE8 2.03 Å, Crystal structure of the von willebrand factor A3 domain in complex with a FAB fragment…

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