4CDL | pdb_00004cdl

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 (Depositor), 0.324 (DCC)
R-Value Work:
0.228 (Depositor), 0.247 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
STEROID DELTA-ISOMERASE	A	141	Pseudomonas putida	Mutation(s): 18 EC: 5.3.3.1
UniProt
Find proteins for P07445 (Pseudomonas putida) Explore P07445 Go to UniProtKB: P07445
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07445
Sequence Annotations 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] mmCIF 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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.297 (Depositor), 0.324 (DCC)
R-Value Work: 0.228 (Depositor), 0.247 (DCC)
R-Value Observed: 0.231 (Depositor)

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

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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
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.2: 2024-10-23
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.