1YEK: Catalytic antibody D2.3 complex

Catalytic antibody D2.3 complex. Determined by X-ray diffraction at 2.1 Å resolution. Released 13 Jan 1999.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,539
Mol. weight: 48.81 kDa
Ligands: NPO, ZN
Released: 13 Jan 1999

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

Secondary structure: helices and β-sheets

1YEK contains 15 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: 9 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
α-helix	99-100A	3
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	10-13	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	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	102-106	5	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
Protein (ig antibody D2.3 (light chain))	L	protein	219	Mus musculus	Q58EU8 (AlphaFold model)
Protein (ig antibody D2.3 (heavy chain))	H	protein	222	Mus musculus	P01863 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1YEK_1 PROTEIN (IG ANTIBODY D2.3 (LIGHT CHAIN)) (chains L)
DIVMTQSPLTLSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIHLVSKLD
SGVPDRITGSGSGTDFTLKISRVEAADLGVYYCVQGTHFPYTFGGGTKLEILRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>1YEK_2 PROTEIN (IG ANTIBODY D2.3 (HEAVY CHAIN)) (chains H)
EMQLQQSGAELLRPGTSVKLSCKTSGYIFTSYWIHWVKQRSGQGLEWIARIYPGTGSTYY
NEKFKGKATLTADKSSSTAYMQLSTLKSEDSAVYFCTRWGFIPVREDYVMDYWGQGTLVT
VSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVL
QSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP

Ligands and cofactors

ID	Name	Formula	Copies
NPO	P-nitrophenol	C6 H5 N O3	1
ZN	Zinc ion	Zn	7

Primary citation

Crossreactivity, efficiency and catalytic specificity of an esterase-like antibody. Gigant, B., Charbonnier, J.B., Eshhar, Z. et al. J Mol Biol (1998) 284:741-750. DOI 10.1006/jmbi.1998.2198 · 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
1ND0 2.45 Å, Cationic cyclization antibody 4C6 complex with transition state analog
2C1O 2.75 Å, ENAIIHis Fab fragment in the free form

Browse structure collections

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