3LEE | pdb_00003lee

Crystal structure of the human squalene synthase complexed with BPH-652

PDB DOI: https://doi.org/10.2210/pdb3LEE/pdb

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

Deposited: 2010-01-14 Released: 2010-12-08
Deposition Author(s): Liu, Y.-L., Lin, F.-Y., Oldfield, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.276 (Depositor), 0.280 (DCC)
R-Value Work:
0.191 (Depositor), 0.190 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Mechanism of Action (and Inhibition) of Head-to-Head Terpene Synthases: A Structural Investigation

Lin, F.-Y., Liu, C.-I., Liu, Y.-L., Zhang, Y., Wang, K., Cao, R., Wang, A.H.J., Oldfield, E.

To be published.

Macromolecule Content

Total Structure Weight: 237.46 kDa
Atom Count: 15,384
Modelled Residue Count: 1,879
Deposited Residue Count: 2,040
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Squalene synthetase	A, B, C, D, E A, B, C, D, E, F	340	Homo sapiens	Mutation(s): 0 Gene Names: FDFT1 EC: 2.5.1.21
UniProt & NIH Common Fund Data Resources
Find proteins for P37268 (Homo sapiens) Explore P37268 Go to UniProtKB: P37268
PHAROS: P37268 GTEx: ENSG00000079459
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P37268
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B65 Query on B65 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain O [auth E] SDF format, chain M [auth D] SDF format, chain Q [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain O [auth E] MOL2 format, chain M [auth D] MOL2 format, chain Q [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain O [auth E] mmCIF format, chain M [auth D] mmCIF format, chain Q [auth F]	G [auth A] I [auth B] K [auth C] M [auth D] O [auth E] G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	(1R)-4-(3-phenoxyphenyl)-1-phosphonobutane-1-sulfonic acid C₁₆ H₁₉ O₇ P S RCGCZPXSRLLKCK-MRXNPFEDSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain N [auth D] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain N [auth D] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F] mmCIF format, chain N [auth D]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth E] H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.276 (Depositor), 0.280 (DCC)
R-Value Work: 0.191 (Depositor), 0.190 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.662	α = 90
b = 153.422	β = 90.5
c = 92.904	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-12-08

Deposition Author(s):

Liu, Y.-L.

Lin, F.-Y.

Oldfield, E.

Revision History (Full details and data files)

Version 1.0: 2010-12-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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Help and Resources

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Crystal structure of the human squalene synthase complexed with BPH-652

Mechanism of Action (and Inhibition) of Head-to-Head Terpene Synthases: A Structural Investigation

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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