3BPT | pdb_00003bpt

Crystal structure of human beta-hydroxyisobutyryl-CoA hydrolase in complex with quercetin

PDB DOI: https://doi.org/10.2210/pdb3BPT/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-12-19 Released: 2008-01-08
Deposition Author(s): Pilka, E.S., Phillips, C., King, O.N.F., Guo, K., von Delft, F., Pike, A.C.W., Arrowsmith, C.H., Weigelt, J., Edwards, A.M., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.197 (Depositor), 0.192 (DCC)
R-Value Work:
0.147 (Depositor), 0.145 (DCC)
R-Value Observed:
0.149 (Depositor)

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 human beta-hydroxyisobutyryl-CoA hydrolase in complex with quercetin.

Pilka, E.S., Phillips, C., King, O.N.F., Guo, K., von Delft, F., Pike, A.C.W., Arrowsmith, C.H., Weigelt, J., Edwards, A.M., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 41.48 kDa
Atom Count: 3,471
Modeled Residue Count: 362
Deposited Residue Count: 363
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyisobutyryl-CoA hydrolase	A	363	Homo sapiens	Mutation(s): 0 Gene Names: HIBCH EC: 3.1.2.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NVY1 (Homo sapiens) Explore Q6NVY1 Go to UniProtKB: Q6NVY1
PHAROS: Q6NVY1 GTEx: ENSG00000198130
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NVY1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QUE Query on QUE 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]	3,5,7,3',4'-PENTAHYDROXYFLAVONE C₁₅ H₁₀ O₇ REFJWTPEDVJJIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
HIU Query on HIU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(2R)-3-HYDROXY-2-METHYLPROPANOIC ACID C₄ H₈ O₃ DBXBTMSZEOQQDU-GSVOUGTGSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.197 (Depositor), 0.192 (DCC)
R-Value Work: 0.147 (Depositor), 0.145 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.096	α = 90
b = 76.642	β = 108.24
c = 55.789	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
SHELXD	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-01-08

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-01-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary