5OMO

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH WITH 3S-HYDROXY-DECANOYL-COA AND 3-KETO-DECANOYL-COA

PDB DOI: https://doi.org/10.2210/pdb5OMO/pdb
Entry: 5OMO supersedes: 5AAJ

Classification: OXIDOREDUCTASE
Organism(s): Rattus norvegicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-08-01 Released: 2017-09-06
Deposition Author(s): Kasaragod, P., Kiema, T.-R., Schmitz, W., Hiltunen, J.K., Wierenga, R.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.228
R-Value Work: 0.193
R-Value Observed: 0.194

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE 1 (RPMFE1) COMPLEXED WITH 3S-HYDROXY-DECANOYL-COA AND 3- KETO-DECANOYL-COA

Kasaragod, P., Balcha, G., Sridhar, S., Schmitz, W., Kiema, T.-R., Hiltunen, J.K., Wierenga, R.K.

Not Published

Macromolecule Content

Total Structure Weight: 165.52 kDa
Atom Count: 11,586
Modelled Residue Count: 1,443
Deposited Residue Count: 1,484
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal bifunctional enzyme	A, B	742	Rattus norvegicus	Mutation(s): 0 Gene Names: Ehhadh EC: 4.2.1.17 (PDB Primary Data), 5.3.3.8 (PDB Primary Data), 1.1.1.35 (PDB Primary Data)
UniProt
Find proteins for P07896 (Rattus norvegicus) Explore P07896 Go to UniProtKB: P07896
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07896
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZOZ (Subject of Investigation/LOI) Query on ZOZ Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	3-KETO-DECANOYL-COA C₃₁ H₅₂ N₇ O₁₈ P₃ S AZCVXMAPLHSIKY-HSJNEKGZSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
HSC (Subject of Investigation/LOI) Query on HSC Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B]	H [auth A], N [auth B]	(S)-3-HYDROXYDECANOYL-COA C₃₁ H₅₀ N₇ O₁₈ P₃ S HIVSMYZAMUNFKZ-PNPVFPMQSA-J		Interactions Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	C [auth A] D [auth A] E [auth A] J [auth B] K [auth B] C [auth A], D [auth A], E [auth A], J [auth B], K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B]	F [auth A], G [auth A], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.228
R-Value Work: 0.193
R-Value Observed: 0.194
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.96	α = 90
b = 125.08	β = 90
c = 223.53	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-09-06

Deposition Author(s):

This entry supersedes: 5AAJ

Revision History (Full details and data files)

Version 1.0: 2017-09-06
Type: Initial release
Version 1.1: 2018-05-02
Changes: Data collection
Version 1.2: 2019-03-20
Changes: Data collection, Database references
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Refinement description

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Help and Resources

5OMO

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH WITH 3S-HYDROXY-DECANOYL-COA AND 3-KETO-DECANOYL-COA

CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE 1 (RPMFE1) COMPLEXED WITH 3S-HYDROXY-DECANOYL-COA AND 3- KETO-DECANOYL-COA

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)