1C1E

CRYSTAL STRUCTURE OF A DIELS-ALDERASE CATALYTIC ANTIBODY 1E9 IN COMPLEX WITH ITS HAPTEN

PDB DOI: https://doi.org/10.2210/pdb1C1E/pdb

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

Deposited: 1999-07-22 Released: 2000-03-01
Deposition Author(s): Xu, J., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.294
R-Value Work: 0.239
R-Value Observed: 0.250

wwPDB Validation 3D Report Full Report

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

Literature

Evolution of shape complementarity and catalytic efficiency from a primordial antibody template.

Xu, J., Deng, Q., Chen, J., Houk, K.N., Bartek, J., Hilvert, D., Wilson, I.A.

(1999) Science 286: 2345-2348

PubMed: 10600746 Search on PubMed
DOI: https://doi.org/10.1126/science.286.5448.2345
Primary Citation of Related Structures:
1C1E

PubMed Abstract:
The crystal structure of an efficient Diels-Alder antibody catalyst at 1.9 angstrom resolution reveals almost perfect shape complementarity with its transition state analog. Comparison with highly related progesterone and Diels-Alderase antibodies that arose from the same primordial germ line template shows the relatively subtle mutational steps that were able to evolve both structural complementarity and catalytic efficiency.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 48.01 kDa
Atom Count: 3,563
Modelled Residue Count: 435
Deposited Residue Count: 435
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATALYTIC ANTIBODY 1E9 (LIGHT CHAIN)	A [auth L]	216	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
CATALYTIC ANTIBODY 1E9 (HEAVY CHAIN)	B [auth H]	219	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ENH Query on ENH Download Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H] mmCIF format, chain D [auth H]	D [auth H]	1,7,8,9,10,10-HEXACHLORO-4-METHYL-4-AZA-TRICYCLO[5.2.1.0(2,6)]DEC-8-ENE-3,5-DIONE C₁₀ H₅ Cl₆ N O₂ DKILHSLDAKXHHE-ASQNABRVSA-N		Interactions Focus chain D [auth H]
MLT Query on MLT Download Ideal Coordinates CCD File SDF format, chain C [auth L] MOL2 format, chain C [auth L] mmCIF format, chain C [auth L]	C [auth L]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain C [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.294
R-Value Work: 0.239
R-Value Observed: 0.250
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.73	α = 90
b = 132.44	β = 90
c = 167.5	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2000-03-01

Deposition Author(s):

Xu, J.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2000-03-01
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2013-01-30
Changes: Non-polymer description
Version 1.4: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary