Macromolecule Content

Total Structure Weight: 16.38 kDa
Atom Count: 1,067
Modelled Residue Count: 126
Deposited Residue Count: 141
Unique protein chains: 1

4CDL

Crystal Structure of Retro-aldolase RA110.4-6 Complexed with Inhibitor 1-(6-methoxy-2-naphthalenyl)-1,3-butanedione

PDB DOI: https://doi.org/10.2210/pdb4CDL/pdb

Classification: ISOMERASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-11-01 Released: 2014-11-12
Deposition Author(s): Pinkas, D.M., Studer, S., Obexer, R., Giger, L., Gruetter, M.G., Baker, D., Hilvert, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.297
R-Value Work: 0.228
R-Value Observed: 0.231

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Active Site Plasticity of a Computationally Designed Retro-Aldolase Enzyme

Studer, S., Obexer, R., Giger, L., Pinkas, D.M., Gruetter, M.G., Baker, D., Hilvert, D.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STEROID DELTA-ISOMERASE	A	141	Pseudomonas putida	Mutation(s): 18 Gene Names: ksi EC: 5.3.3.1
UniProt
Find proteins for P07445 (Pseudomonas putida) Explore P07445 Go to UniProtKB: P07445
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07445
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LLK Query on LLK Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	(2E)-1-(6-methoxynaphthalen-2-yl)but-2-en-1-one C₁₅ H₁₄ O₂ MDAHFYAQSIDRGG-ONEGZZNKSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.297
R-Value Work: 0.228
R-Value Observed: 0.231
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.58	α = 90
b = 51.58	β = 90
c = 198.64	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-11-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-12
Type: Initial release
Version 2.0: 2019-10-23
Changes: Atomic model, Data collection, Derived calculations, Other

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.