PDB-9cy2: Crystal structure of human farnesyl pyrophosphate synthase in com...

ID or keywords:

Entry

Database: PDB / ID: 9cy2

Title

Crystal structure of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, JDS05120

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: 2.2 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, JDS05120
Authors: Pandya, V.R. / Park, J.

History

Deposition	Aug 1, 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	9cy2.cif.gz	197.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9cy2.ent.gz	122.2 KB	Display	PDB format
PDBx/mmJSON format	9cy2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9cy2_validation.pdf.gz	691.5 KB	Display	wwPDB validaton report
Full document	9cy2_full_validation.pdf.gz	692.4 KB	Display
Data in XML	9cy2_validation.xml.gz	17 KB	Display
Data in CIF	9cy2_validation.cif.gz	23 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cy/9cy2 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/9cy2	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

43.6 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
87.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	110.950, 110.950, 73.900
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-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-JD5 / [({5-[4-(cyclopropyloxy)phenyl]pyridin-3-yl}amino)methanediyl]bis(phosphonic acid) Mass: 400.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₁₈N₂O₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.64 Å³/Da / Density % sol: 53.33 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.085 M HEPES (pH 7.5), 17% (w/v) PEG 10000, 6.8% (v/v) ethylene glycol, 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: Sep 19, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 2.2→49.62 Å / Num. obs: 23662 / % possible obs: 98.9 % / Redundancy: 8.9 % / B_iso Wilson estimate: 59.516 Å² / R_merge(I) obs: 0.041 / R_pim(I) all: 0.015 / R_rim(I) all: 0.045 / Net I/σ(I): 24.7
Reflection shell	Resolution: 2.2→2.26 Å / Redundancy: 8.6 % / R_merge(I) obs: 1.004 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1696 / R_pim(I) all: 0.374 / R_rim(I) all: 1.126 / % possible all: 97.2

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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: 2.2→49.618 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.94 / SU B: 21.083 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.196
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2462	1197	5.064 %	Random
R_work	0.1882	22441	-	-
all	0.191	-	-	-
obs	-	23638	98.541 %	-

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: 81.006 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.027 Å²	0 Å²	-0 Å²
2-	-	-5.027 Å²	0 Å²
3-	-	-	10.053 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→49.618 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2674	0	31	96	2801

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	2762
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2572
X-RAY DIFFRACTION	r_angle_refined_deg	1.435	1.827	3754
X-RAY DIFFRACTION	r_angle_other_deg	0.502	1.746	5892
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.031	5	334
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.39	5	16
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.331	10	441
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.044	10	130
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	419
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3225
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	646
X-RAY DIFFRACTION	r_nbd_refined	0.231	0.2	647
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	2276
X-RAY DIFFRACTION	r_nbtor_refined	0.193	0.2	1393
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.072	0.2	1428
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.197	0.2	92
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.035	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.151	0.2	56
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.062	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	3.298	5.041	1348
X-RAY DIFFRACTION	r_mcbond_other	3.295	5.042	1348
X-RAY DIFFRACTION	r_mcangle_it	4.771	9.042	1678
X-RAY DIFFRACTION	r_mcangle_other	4.77	9.043	1679
X-RAY DIFFRACTION	r_scbond_it	4.393	5.607	1414
X-RAY DIFFRACTION	r_scbond_other	4.394	5.611	1415
X-RAY DIFFRACTION	r_scangle_it	6.592	10.17	2073
X-RAY DIFFRACTION	r_scangle_other	6.59	10.173	2074
X-RAY DIFFRACTION	r_lrange_it	9.381	49.232	3228
X-RAY DIFFRACTION	r_lrange_other	9.385	49.244	3229

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
2.2-2.257	0.391	90	0.418	1603	0.417	1744	0.714	0.646	97.0757	0.359
2.257-2.319	0.346	73	0.337	1603	0.337	1694	0.759	0.695	98.9374	0.269
2.319-2.386	0.37	83	0.307	1543	0.31	1640	0.806	0.759	99.1463	0.245
2.386-2.459	0.311	73	0.294	1523	0.294	1607	0.806	0.805	99.3155	0.238
2.459-2.54	0.279	60	0.295	1487	0.295	1560	0.808	0.821	99.1667	0.238
2.54-2.628	0.28	76	0.257	1410	0.258	1497	0.841	0.885	99.2652	0.207
2.628-2.727	0.256	74	0.226	1382	0.228	1464	0.946	0.935	99.4536	0.181
2.727-2.838	0.214	82	0.189	1307	0.19	1409	0.967	0.961	98.5806	0.151
2.838-2.964	0.251	67	0.168	1266	0.172	1347	0.955	0.973	98.9607	0.136
2.964-3.108	0.26	61	0.17	1218	0.174	1289	0.954	0.977	99.2242	0.144
3.108-3.276	0.206	60	0.162	1163	0.164	1234	0.973	0.981	99.1086	0.142
3.276-3.473	0.188	52	0.164	1107	0.166	1173	0.975	0.981	98.8065	0.147
3.473-3.712	0.23	63	0.17	1033	0.173	1117	0.966	0.983	98.12	0.163
3.712-4.007	0.225	58	0.155	958	0.159	1029	0.967	0.984	98.7366	0.151
4.007-4.387	0.244	59	0.141	883	0.147	961	0.963	0.987	98.0229	0.144
4.387-4.9	0.203	58	0.135	809	0.139	883	0.971	0.988	98.188	0.146
4.9-5.649	0.207	34	0.167	727	0.169	780	0.963	0.983	97.5641	0.176
5.649-6.896	0.282	39	0.216	620	0.221	676	0.956	0.969	97.4852	0.218
6.896-9.66	0.269	20	0.17	502	0.174	539	0.971	0.983	96.846	0.205
9.66-49.618	0.302	15	0.228	297	0.231	341	0.953	0.963	91.4956	0.285

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	11.4055	2.4206	-6.4295	3.557	0.2886	10.8963	-0.4429	1.3101	-0.1347	-0.3876	0.6078	0.6347	0.8728	-1.4288	-0.165	0.2898	-0.1578	-0.2004	0.4248	0.0055	0.3761	0.6343	81.1274	9.8442
2	10.3578	0.5102	-6.0828	2.3906	0.7256	5.7189	0.1894	0.9925	-0.1398	-0.4917	0.047	0.5	-0.0559	-0.9327	-0.2364	0.1864	-0.082	-0.1718	0.2265	0.0639	0.2975	5.4152	84.03	12.0358
3	9.4926	-3.5945	-0.7687	4.3343	-0.3849	2.819	-0.0259	0.3611	-0.3347	-0.4225	0.1112	0.3545	0.2519	-0.3846	-0.0853	0.088	-0.0688	-0.031	0.0815	0.009	0.0321	12.1054	84.2799	14.5193
4	5.4664	-0.364	2.1618	4.8363	-3.2069	6.6884	0.0906	-0.7076	-0.286	0.4654	-0.0849	-0.1013	-0.0248	0.3442	-0.0057	0.0855	-0.0236	0.0181	0.2153	-0.0012	0.0648	16.3156	85.8957	31.9598
5	7.6092	-2.645	1.6999	5.4602	-3.0858	4.3666	0.1268	-0.4846	-0.888	0.1515	-0.089	0.1297	0.4477	0.2708	-0.0377	0.1437	-0.0229	0.0358	0.2915	0.1278	0.3515	8.0865	78.0604	34.5796
6	8.5528	-4.0423	2.4549	3.7574	-1.7692	2.8091	0.1345	-0.6208	-0.9965	0.3076	0.0105	0.0017	0.4786	0.2854	-0.145	0.3477	-0.0409	0.0249	0.4706	0.2182	0.5753	8.7662	71.1888	40.5288

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	F	8 - 30
2	X-RAY DIFFRACTION	2	ALL	F	34 - 76
3	X-RAY DIFFRACTION	3	ALL	F	77 - 151
4	X-RAY DIFFRACTION	4	ALL	F	152 - 205
5	X-RAY DIFFRACTION	5	ALL	F	206 - 279
6	X-RAY DIFFRACTION	6	ALL	F	280 - 350

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