4Q23

The role of threonine 201 and tyrosine 204 in the human farnesyl pyrophosphate synthase catalytic mechanism and the mode of inhibition by the nitrogen-containing bisphosphonates

PDB DOI: https://doi.org/10.2210/pdb4Q23/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-04-05 Released: 2015-03-18
Deposition Author(s): Tsoumpra, M.K., Muniz, J.R.C., Barnett, B.L., Kwaasi, A.A., Pilka, E.S., Kavanagh, K.L., Evdokimov, A., Walter, R.L., Ebetino, F.H., von Delft, F., Oppermann, U., Russell, R.G.G., Dunford, J.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.223
R-Value Work: 0.192
R-Value Observed: 0.193

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The role of threonine 201 and tyrosine 204 in the human farnesyl pyrophosphate synthase catalytic mechanism and the mode of inhibition by the nitrogen-containing bisphosphonates

Tsoumpra, M.K., Muniz, J.R.C., Barnett, B.L., Kwaasi, A.A., Pilka, E.S., Kavanagh, K.L., Evdokimov, A., Walter, R.L., Ebetino, F.H., von Delft, F., Oppermann, U., Russell, R.G.G., Dunford, J.E.

To be published.

Macromolecule Content

Total Structure Weight: 43.57 kDa
Atom Count: 2,821
Modelled Residue Count: 337
Deposited Residue Count: 375
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Farnesyl pyrophosphate synthase	A	375	Homo sapiens	Mutation(s): 1 Gene Names: FDPS, FPS, KIAA1293 EC: 2.5.1.10 (PDB Primary Data), 2.5.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P14324 (Homo sapiens) Explore P14324 Go to UniProtKB: P14324
PHAROS: P14324 GTEx: ENSG00000160752
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14324
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RIS Query on RIS 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]	1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID C₇ H₁₁ N O₇ P₂ IIDJRNMFWXDHID-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.223
R-Value Work: 0.192
R-Value Observed: 0.193
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.36	α = 90
b = 111.36	β = 90
c = 67.6	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-03-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-03-18
Type: Initial release
Version 1.1: 2018-01-31
Changes: Database references, Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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4Q23

The role of threonine 201 and tyrosine 204 in the human farnesyl pyrophosphate synthase catalytic mechanism and the mode of inhibition by the nitrogen-containing bisphosphonates

The role of threonine 201 and tyrosine 204 in the human farnesyl pyrophosphate synthase catalytic mechanism and the mode of inhibition by the nitrogen-containing bisphosphonates

Entity ID: 1

UniProt & NIH Common Fund Data Resources

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)