3CFD: Purple-fluorescent antibody EP2-25C10

Purple-fluorescent antibody EP2-25C10 in complex with its stilbene hapten. Determined by X-ray diffraction at 2.5 Å resolution. Released 18 Mar 2008.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Mus musculus
Chains: 4
Atoms: 6,824
Mol. weight: 95.53 kDa
Ligands: SPB
Released: 18 Mar 2008

Explore 3CFD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3CFD contains 23 α-helices and 84 β-strands across 4 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 A: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	11
β-strand	10-13	4	12
β-strand	19-25	7	11
β-strand	33-38	6	12
β-strand	44-49	6	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-67	6	11
β-strand	70-75	6	11
α-helix	80-82	3
β-strand	84-90	7	12
α-helix	96	1
β-strand	97-98	2	12
β-strand	102-106	5	12
β-strand	111	1	13
β-strand	114-118	5	14
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	14
β-strand	140	1	13
β-strand	145-150	6	15
β-strand	153-155	3	15
β-strand	159-163	5	14
α-helix	164-167	4
β-strand	173-182	10	14
α-helix	183-187	5
β-strand	191-197	7	15
β-strand	205-210	6	15

Chain B: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	16
β-strand	11-12	2	17
β-strand	18-25	8	16
β-strand	34-40	8	12
β-strand	44-52	9	12
β-strand	57-59	3	12
β-strand	67-72	6	16
β-strand	77-82	6	16
α-helix	84-86	3
β-strand	88-95	8	12
β-strand	100C-103	4	12
β-strand	107-109	3	12
β-strand	110-111	2	17
α-helix	114-116	3
β-strand	117	1	18
α-helix	118-119	2
β-strand	120-124	5	19
β-strand	137-147	11	19
β-strand	148	1	18
β-strand	153-162	5	20
β-strand	169-179	10	19
β-strand	184-194	11	19
β-strand	206-212	6	20
β-strand	217-222	6	20

Chain H: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
β-strand	34-39	7	2
β-strand	45-52	8	2
β-strand	57-59	3	2
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-95	8	2
β-strand	100C-103	4	2
β-strand	107-109	3	2
β-strand	110-111	2	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	153-162	5	10
β-strand	169-179	10	9
β-strand	184-194	11	9
α-helix	195-198	3
β-strand	206-212	6	10
α-helix	213-215	3
β-strand	217-222	6	10

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	10-13	4	2
β-strand	19-25	7	1
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
α-helix	107	1
β-strand	111	1	3
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	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	183-186	4
β-strand	191-197	7	5
β-strand	205-210	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Purple-fluorescent antibody EP2-25C10-kappa light chain	A, L	protein	214	Mus musculus	P01837 (AlphaFold model)
Purple-fluorescent antibody EP2-25C10-IGG2B heavy chain	B, H	protein	220	Mus musculus	P01867 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>3CFD_1 PURPLE-FLUORESCENT ANTIBODY EP2-25C10-KAPPA LIGHT CHAIN (chains A, L)
DIQMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPS
RFSGSGSGTDYSLTISNLDQDDIATYFCQQGTTLPPTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B, H), FASTA

>3CFD_2 PURPLE-FLUORESCENT ANTIBODY EP2-25C10-IGG2B HEAVY CHAIN (chains B, H)
EVQLQESGPGLVKPSQSLSLTCTVTGYSITSDYAWNWLRQLPGNKLEWMGYISYSGRIRY
NPSLKRRISITRDTSKNQFFLQLNSVTTEDTATYYCARSDYGNYGRGDYWGQGTSVTVSS
AKTTPPSVYPLAPGCGDTTGSSVTSGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSG
LYTMSSSVTVPSSTWPSETVTCSVAHPASSTTVDKKLEPS

Ligands and cofactors

ID	Name	Formula	Copies
SPB	4-(4-styryl-phenylcarbamoyl)-butyric acid	C19 H19 N O3	2

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

Primary citation

Deeply inverted electron-hole recombination in a luminescent antibody-stilbene complex. Debler, E.W., Kaufmann, G.F., Meijler, M.M. et al. Science (2008) 319:1232-1235. DOI 10.1126/science.1153445 · 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…

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