PDB-9cyz: Crystal structure of human farnesyl pyrophosphate synthase in com...

ID or keywords:

Entry

Database: PDB / ID: 9cyz

Title

Crystal structure of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, CL02134

Components

Farnesyl pyrophosphate synthase

Keywords

TRANSFERASE / enzyme-ligand complex / cryptic pocket binder / isoprenoid biosynthesis

Function / homology

Function and homology information

geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / peroxisome ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.302 Å

Authors

Pandya, V.R. / Park, J.

Funding support

Canada, 1items

Citation

Journal: To Be Published
Title: Crystal structure of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, CL02134
Authors: Pandya, V.R. / Park, J.

History

Deposition	Aug 3, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 29, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9cyz.cif.gz	198.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9cyz.ent.gz	123.4 KB	Display	PDB format
PDBx/mmJSON format	9cyz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9cyz_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	9cyz_full_validation.pdf.gz	1.2 MB	Display
Data in XML	9cyz_validation.xml.gz	18 KB	Display
Data in CIF	9cyz_validation.cif.gz	24.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cy/9cyz ftp://data.pdbj.org/pub/pdb/validation_reports/cy/9cyz	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#201 - Sep 2016 Isoprene Synthase similarity (8) #96 - Dec 2007 Oxidosqualene Cyclase similarity (1)

Deposited unit

F: Farnesyl pyrophosphate synthase

hetero molecules

44.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

F: Farnesyl pyrophosphate synthase

hetero molecules

F: Farnesyl pyrophosphate synthase

hetero molecules

defined by author&software
Evidence: gel filtration
89.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	110.750, 110.750, 77.500
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Farnesyl pyrophosphate synthase / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl ...FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Geranyltranstransferase Mass: 43144.980 Da / Num. of mol.: 1 / Fragment: residues 67-419 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-YL2 / ({[6-(4-cyclopropylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}methanediyl)bis(phosphonic acid) Mass: 441.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₆H₁₇N₃O₆P₂S / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.75 Å³/Da / Density % sol: 55.34 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.085 M tri-Sodium citrate (pH 5.6), 0.425 M Ammonium sulfate, 0.85 M Lithium sulfate, 15% (v/v) Glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 21, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 2.3→55.09 Å / Num. obs: 21853 / % possible obs: 99.6 % / Redundancy: 9.7 % / B_iso Wilson estimate: 56.757 Å² / R_merge(I) obs: 0.046 / R_pim(I) all: 0.016 / R_rim(I) all: 0.05 / Net I/σ(I): 28.4
Reflection shell	Resolution: 2.3→2.36 Å / Redundancy: 9.8 % / R_merge(I) obs: 1.043 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1593 / R_pim(I) all: 0.352 / R_rim(I) all: 1.155 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
XSCALE		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 2.302→55.086 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.96 / SU B: 17.273 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.187
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2132	1130	5.181 %	Random
R_work	0.1681	20680	-	-
all	0.17	-	-	-
obs	0.1704	21810	99.475 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 71.803 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.807 Å²	-0 Å²	-0 Å²
2-	-	-4.807 Å²	-0 Å²
3-	-	-	9.614 Å²

Refinement step

Cycle: LAST / Resolution: 2.302→55.086 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2675	0	100	106	2881

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	2842
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2610
X-RAY DIFFRACTION	r_angle_refined_deg	1.627	1.833	3877
X-RAY DIFFRACTION	r_angle_other_deg	0.521	1.741	5986
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.249	5	334
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.402	5	18
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.436	10	446
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.763	10	131
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	430
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3269
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	654
X-RAY DIFFRACTION	r_nbd_refined	0.236	0.2	657
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	2324
X-RAY DIFFRACTION	r_nbtor_refined	0.196	0.2	1407
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1411
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.18	0.2	116
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.015	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.249	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.166	0.2	85
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.157	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	3.118	4.652	1345
X-RAY DIFFRACTION	r_mcbond_other	3.109	4.652	1345
X-RAY DIFFRACTION	r_mcangle_it	4.463	8.35	1676
X-RAY DIFFRACTION	r_mcangle_other	4.462	8.352	1677
X-RAY DIFFRACTION	r_scbond_it	4.366	5.307	1497
X-RAY DIFFRACTION	r_scbond_other	4.365	5.309	1498
X-RAY DIFFRACTION	r_scangle_it	6.369	9.648	2192
X-RAY DIFFRACTION	r_scangle_other	6.368	9.649	2193
X-RAY DIFFRACTION	r_lrange_it	8.228	47.507	3371
X-RAY DIFFRACTION	r_lrange_other	8.227	47.513	3372

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.302-2.362	0.351	76	0.325	1508	0.326	1592	0.867	0.813	99.4975	0.277
2.362-2.427	0.284	84	0.314	1451	0.312	1541	0.87	0.854	99.6106	0.271
2.427-2.497	0.323	91	0.274	1424	0.277	1520	0.85	0.895	99.6711	0.23
2.497-2.573	0.294	71	0.246	1376	0.248	1460	0.936	0.929	99.1096	0.202
2.573-2.658	0.236	85	0.199	1327	0.201	1417	0.951	0.963	99.6471	0.166
2.658-2.751	0.218	65	0.185	1294	0.187	1369	0.966	0.965	99.2695	0.149
2.751-2.854	0.283	56	0.169	1268	0.174	1331	0.952	0.977	99.4741	0.142
2.854-2.97	0.238	60	0.172	1219	0.176	1285	0.961	0.978	99.5331	0.147
2.97-3.102	0.234	53	0.176	1183	0.178	1239	0.966	0.979	99.7579	0.15
3.102-3.253	0.255	74	0.161	1105	0.166	1182	0.965	0.983	99.7462	0.146
3.253-3.428	0.226	57	0.175	1059	0.178	1120	0.964	0.98	99.6429	0.16
3.428-3.635	0.242	52	0.167	1020	0.171	1078	0.967	0.984	99.4434	0.158
3.635-3.885	0.191	47	0.152	967	0.154	1016	0.979	0.985	99.8031	0.147
3.885-4.195	0.182	59	0.135	883	0.138	946	0.973	0.988	99.5772	0.136
4.195-4.592	0.208	48	0.135	830	0.139	882	0.975	0.988	99.5465	0.139
4.592-5.13	0.185	56	0.132	740	0.135	800	0.978	0.989	99.5	0.142
5.13-5.915	0.211	32	0.145	680	0.148	714	0.973	0.986	99.7199	0.153
5.915-7.224	0.204	28	0.164	591	0.166	620	0.983	0.984	99.8387	0.172
7.224-10.129	0.118	25	0.124	463	0.123	496	0.99	0.991	98.3871	0.144
10.129-55.086	0.242	11	0.231	292	0.231	314	0.966	0.965	96.4968	0.291

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.4927	0.367	-2.0762	2.5773	-0.2573	2.7794	-0.0237	0.4578	-0.2499	-0.4187	0.223	0.4269	0.2744	-0.6015	-0.1993	0.0987	-0.0854	-0.1052	0.1412	0.0702	0.1258	9.1758	84.6715	16.442
2	4.0672	-0.9316	0.6891	4.4514	-2.278	3.7857	0.04	-0.4191	-0.4088	0.3099	-0.0394	-0.0102	0.3048	0.2807	-0.0006	0.1367	-0.0235	0.0147	0.292	0.057	0.088	9.937	75.9031	39.1623

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	F	8 - 179
2	X-RAY DIFFRACTION	2	ALL	F	184 - 350

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