2G2R

Green-fluorescent antibody 11G10 in complex with its hapten (nitro-stilbene derivative)

PDB DOI: https://doi.org/10.2210/pdb2G2R/pdb

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

Deposited: 2006-02-16 Released: 2006-12-05
Deposition Author(s): Debler, E.W., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.250
R-Value Work: 0.203
R-Value Observed: 0.205

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The Effects of Antibodies on Stilbene Excited-State Energetics.

Tian, F., Debler, E.W., Millar, D.P., Deniz, A.A., Wilson, I.A., Schultz, P.G.

(2006) Angew Chem Int Ed Engl 45: 7763-7765

PubMed: 17089439 Search on PubMed
DOI: https://doi.org/10.1002/anie.200602720
Primary Citation of Related Structures:
2G2R

Organizational Affiliation

Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, SR202, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 96.76 kDa
Atom Count: 6,917
Modelled Residue Count: 876
Deposited Residue Count: 876
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green-fluorescent antibody (11G10)-light chain	A [auth L], C [auth A]	219	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Green-fluorescent antibody (11G10)-heavy chain	B [auth H], D [auth B]	219	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P84751 (Mus musculus) Explore P84751 Go to UniProtKB: P84751
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P84751
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TNS Query on TNS Download Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain H [auth A] MOL2 format, chain F [auth L] MOL2 format, chain H [auth A] mmCIF format, chain F [auth L] mmCIF format, chain H [auth A]	F [auth L], H [auth A]	N-(TRANS-4'-NITRO-4-STILBENYL)-N-METHYL-5-AMINO-PENTANOIC ACID C₂₀ H₂₂ N₂ O₄ QLLZAVDYYAQESE-AATRIKPKSA-N		Interactions Focus chain F [auth L] Focus chain H [auth A] Interactions & Density Focus chain F [auth L] Focus chain H [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth L] SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth L] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth L] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B]	E [auth L], G [auth A], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth L] Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth L] Focus chain G [auth A] Focus chain I [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
TNS	PDBBind: 2G2R	Kd: 13 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.250
R-Value Work: 0.203
R-Value Observed: 0.205
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.788	α = 90
b = 53.761	β = 94.64
c = 110.39	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-12-05

Deposition Author(s):

Debler, E.W.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2006-12-05
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary