1LSO | pdb_00001lso

Crystal Structure of the S137A mutant of L-3-Hydroxyacyl-CoA Dehydrogenase in Complex with NAD

PDB DOI: https://doi.org/10.2210/pdb1LSO/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2002-05-17 Released: 2004-02-03
Deposition Author(s): Barycki, J.J., Banaszak, L.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.285 (Depositor), 0.283 (DCC)
R-Value Work:
0.220 (Depositor), 0.220 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1LSO

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of the S137A mutant of L-3-Hydroxyacyl-CoA Dehydrogenase in Complex with NAD

Barycki, J.J., Banaszak, L.J.

To be published.

Macromolecule Content

Total Structure Weight: 67.03 kDa
Atom Count: 4,645
Modeled Residue Count: 582
Deposited Residue Count: 604
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-HYDROXYACYL-COA DEHYDROGENASE	A, B	302	Homo sapiens	Mutation(s): 1 Gene Names: HCDH EC: 1.1.1.35
UniProt & NIH Common Fund Data Resources
Find proteins for Q16836 (Homo sapiens) Explore Q16836 Go to UniProtKB: Q16836
PHAROS: Q16836 GTEx: ENSG00000138796
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16836
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	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: 2.60 Å
R-Value Free: 0.285 (Depositor), 0.283 (DCC)
R-Value Work: 0.220 (Depositor), 0.220 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.361	α = 90
b = 86.452	β = 90
c = 167.687	γ = 90

Software Package:

Software Name	Purpose
Crystal	data collection
Crystal	data reduction
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-02-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-02-03
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-04-04
Changes: Data collection
Version 1.4: 2021-10-27
Changes: Database references, Derived calculations
Version 1.5: 2024-02-14
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.