2GJZ | pdb_00002gjz

Structure of Catalytic Elimination Antibody 13G5 from a crystal in space group P2(1)

PDB DOI: https://doi.org/10.2210/pdb2GJZ/pdb

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

Deposited: 2006-03-31 Released: 2007-02-06
Deposition Author(s): Debler, E.W., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.250 (Depositor), 0.246 (DCC)
R-Value Work:
0.213 (Depositor), 0.209 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Bifunctional Catalysis of Proton Transfer at an Antibody Active Site.

Muller, R., Debler, E.W., Steinmann, M., Seebeck, F.P., Wilson, I.A., Hilvert, D.

(2007) J Am Chem Soc 129: 460-461

PubMed: 17226987 Search on PubMed
DOI: https://doi.org/10.1021/ja066578b
Primary Citation Related Structures:
2GJZ, 2GK0

Organizational Affiliation

Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg HCI F 339, CH-8093 Zürich, Switzerland.

Macromolecule Content

Total Structure Weight: 95.56 kDa
Atom Count: 6,706
Modeled Residue Count: 876
Deposited Residue Count: 876
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalytic elimination antibody 13G5 light chain	A [auth L], C [auth A]	217	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q65ZC0 (Mus musculus) Explore Q65ZC0 Go to UniProtKB: Q65ZC0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q65ZC0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalytic elimination antibody 13G5 heavy chain	B [auth H], D [auth B]	221	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth L] SDF format, chain I [auth L] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain K [auth H] SDF format, chain J [auth H] SDF format, chain H [auth L] SDF format, chain G [auth L] SDF format, chain F [auth L] MOL2 format, chain E [auth L] MOL2 format, chain I [auth L] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth H] MOL2 format, chain J [auth H] MOL2 format, chain H [auth L] MOL2 format, chain G [auth L] MOL2 format, chain F [auth L] mmCIF format, chain E [auth L] mmCIF format, chain I [auth L] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth H] mmCIF format, chain J [auth H] mmCIF format, chain H [auth L] mmCIF format, chain G [auth L] mmCIF format, chain F [auth L]	E [auth L] F [auth L] G [auth L] H [auth L] I [auth L] E [auth L], F [auth L], G [auth L], H [auth L], I [auth L], J [auth H], K [auth H], L [auth A], M [auth B], N [auth B], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.250 (Depositor), 0.246 (DCC)
R-Value Work: 0.213 (Depositor), 0.209 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.209	α = 90
b = 73.495	β = 96.33
c = 130.475	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-02-06

Deposition Author(s):

Debler, E.W.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2007-02-06
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, 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