4KPJ

Crystal Structure of Farnesyl Pyrophosphate Synthase (Y204A) Mutant complexed with Mg, Pamidronate

PDB DOI: https://doi.org/10.2210/pdb4KPJ/pdb

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

Deposited: 2013-05-13 Released: 2014-04-30
Deposition Author(s): Barnett, B.L., Tsoumpra, M.K., Muniz, J.R.C., Walter, R.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.215
R-Value Work: 0.172
R-Value Observed: 0.174

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Farnesyl Pyrophosphate Synthase (Y204A) Mutant complexed with Mg, Pamidronate

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

To be published.

Macromolecule Content

Total Structure Weight: 43.73 kDa
Atom Count: 3,084
Modelled Residue Count: 338
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
210 Query on 210 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]	PAMIDRONATE C₃ H₁₁ N O₇ P₂ WRUUGTRCQOWXEG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [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]

Binding Affinity Annotations
ID	Source	Binding Affinity
210	BindingDB: 4KPJ	Ki: min: 55.9, max: 331.4 (nM) from 3 assay(s)
210	BindingDB: 4KPJ	IC50: min: 200, max: 1932 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.215
R-Value Work: 0.172
R-Value Observed: 0.174
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.31	α = 90
b = 111.31	β = 90
c = 66.6	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-04-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-30
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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4KPJ

Crystal Structure of Farnesyl Pyrophosphate Synthase (Y204A) Mutant complexed with Mg, Pamidronate

Crystal Structure of Farnesyl Pyrophosphate Synthase (Y204A) Mutant complexed with Mg, Pamidronate

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)