3CFD | pdb_00003cfd

Purple-fluorescent antibody EP2-25C10 in complex with its stilbene hapten

PDB DOI: https://doi.org/10.2210/pdb3CFD/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Mutation(s): No

Deposited: 2008-03-03 Released: 2008-03-18
Deposition Author(s): Debler, E.W., Heine, A., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.243 (Depositor), 0.233 (DCC)
R-Value Work:
0.211 (Depositor)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Deeply inverted electron-hole recombination in a luminescent antibody-stilbene complex.

Debler, E.W., Kaufmann, G.F., Meijler, M.M., Heine, A., Mee, J.M., Pljevaljcic, G., Di Bilio, A.J., Schultz, P.G., Millar, D.P., Janda, K.D., Wilson, I.A., Gray, H.B., Lerner, R.A.

(2008) Science 319: 1232-1235

PubMed: 18309081 Search on PubMed
DOI: https://doi.org/10.1126/science.1153445
Primary Citation Related Structures:
3CFB, 3CFC, 3CFD, 3CFE

PubMed Abstract:
The blue-emissive antibody EP2-19G2 that has been elicited against trans-stilbene has unprecedented ability to produce bright luminescence and has been used as a biosensor in various applications. We show that the prolonged luminescence is not stilbene fluorescence. Instead, the emissive species is a charge-transfer excited complex of an anionic stilbene and a cationic, parallel pi-stacked tryptophan. Upon charge recombination, this complex generates exceptionally bright blue light. Complex formation is enabled by a deeply penetrating ligand-binding pocket, which in turn results from a noncanonical interface between the two variable domains of the antibody.

Organizational Affiliation

Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 95.53 kDa
Atom Count: 6,824
Modeled Residue Count: 865
Deposited Residue Count: 868
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PURPLE-FLUORESCENT ANTIBODY EP2-25C10-KAPPA LIGHT CHAIN	A [auth L], C [auth A]	214	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01837 (Mus musculus) Explore P01837 Go to UniProtKB: P01837
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01837
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PURPLE-FLUORESCENT ANTIBODY EP2-25C10-IGG2B HEAVY CHAIN	B [auth H], D [auth B]	220	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01867 (Mus musculus) Explore P01867 Go to UniProtKB: P01867
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01867
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SPB Query on SPB Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth H] MOL2 format, chain G [auth B] MOL2 format, chain E [auth H] mmCIF format, chain G [auth B] mmCIF format, chain E [auth H]	E [auth H], G [auth B]	4-(4-STYRYL-PHENYLCARBAMOYL)-BUTYRIC ACID C₁₉ H₁₉ N O₃ FTXJWRRYLLRFMG-MDZDMXLPSA-N		Interactions Focus chain E [auth H] Focus chain G [auth B] Interactions & Density Focus chain E [auth H] Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth H] MOL2 format, chain F [auth H] mmCIF format, chain F [auth H]	F [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth H] Interactions & Density Focus chain F [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.243 (Depositor), 0.233 (DCC)
R-Value Work: 0.211 (Depositor)
R-Value Observed: 0.212 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.99	α = 91.98
b = 72.48	β = 106.11
c = 77.23	γ = 114.15

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-03-18

Deposition Author(s):

Debler, E.W.

Heine, A.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2008-03-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-09
Changes: Structure summary