7N09 | pdb_00007n09

Structural basis for branched substrate selectivity in a ketoreductase from Ascaris suum

PDB DOI: https://doi.org/10.2210/pdb7N09/pdb
Entry: 7N09 supersedes: 6U5I

Classification: OXIDOREDUCTASE
Organism(s): Ascaris suum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-05-25 Released: 2021-08-11
Deposition Author(s): Dong, H., Chang, M.C.Y.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.177 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural Basis for Branched Substrate Selectivity in a Ketoreductase from Ascaris suum

Dong, H., Chang, M.C.Y.

(2021) ACS Catal 11: 8948-8955

DOI: https://doi.org/10.1021/acscatal.1c01642

Macromolecule Content

Total Structure Weight: 60.06 kDa
Atom Count: 4,261
Modeled Residue Count: 518
Deposited Residue Count: 554
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyacyl-CoA dehydrogenase type-2	A, B	277	Ascaris suum	Mutation(s): 0 EC: 1.1.1.53 (UniProt), 1.1.1.62 (UniProt)
UniProt
Find proteins for F1L0H2 (Ascaris suum) Explore F1L0H2 Go to UniProtKB: F1L0H2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F1L0H2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.177 (Depositor), 0.180 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.542	α = 90
b = 54.942	β = 131.039
c = 89.27	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
BALBES	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-08-11

Deposition Author(s):

This entry supersedes: 6U5I

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1413862

Revision History (Full details and data files)

Version 1.0: 2021-08-11
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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.