PDB-9mdf: Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in c...

ID or keywords:

Entry

Database: PDB / ID: 9mdf

Title

Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with NADP and Indomethacin

Components

Prostaglandin reductase 1

Keywords

OXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Prostaglandin reductase 1 / indomethacin

Function / homology

Function and homology information

leukotriene B4 metabolic process / 13-lipoxin reductase activity / leukotriene B4 12-hydroxy dehydrogenase activity / lipoxin A4 metabolic process / 2-alkenal reductase [NAD(P)+] / 2-alkenal reductase (NADPH) activity / 13,14-dehydro-15-oxoprostaglandin 13-reductase / 15-oxoprostaglandin 13-reductase [NAD(P)+] activity / Biosynthesis of Lipoxins (LX) / leukotriene metabolic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with NADP and Indomethacin
Authors: Lovell, S. / Cooper, A. / Liu, L. / Battaile, K.P.

History

Deposition	Dec 5, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 10, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9mdf.cif.gz	516.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9mdf.ent.gz	425.8 KB	Display	PDB format
PDBx/mmJSON format	9mdf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9mdf_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	9mdf_full_validation.pdf.gz	2.5 MB	Display
Data in XML	9mdf_validation.xml.gz	60.7 KB	Display
Data in CIF	9mdf_validation.cif.gz	77.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/md/9mdf ftp://data.pdbj.org/pub/pdb/validation_reports/md/9mdf	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	#17 - May 2001 Cyclooxygenase similarity (1) #13 - Jan 2001 Alcohol Dehydrogenase similarity (5) #32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Prostaglandin reductase 1

B: Prostaglandin reductase 1

C: Prostaglandin reductase 1

D: Prostaglandin reductase 1

hetero molecules

148 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	84.822, 94.720, 87.332
Angle α, β, γ (deg.)	90.00, 94.88, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Prostaglandin reductase 1 / PRG-1 / 15-oxoprostaglandin 13-reductase / Dithiolethione-inducible gene 1 protein / D3T-inducible ...PRG-1 / 15-oxoprostaglandin 13-reductase / Dithiolethione-inducible gene 1 protein / D3T-inducible gene 1 protein / DIG-1 / Leukotriene B4 12-hydroxydehydrogenase / NAD(P)H-dependent alkenal/one oxidoreductase Mass: 35968.734 Da / Num. of mol.: 4 / Fragment: T4-A329 / Mutation: A27S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTGR1, LTB4DH / Plasmid: HosaA.00871.a.A2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q14914, 13,14-dehydro-15-oxoprostaglandin 13-reductase, 2-alkenal reductase [NAD(P)+]

#1: Protein

Prostaglandin reductase 1 / PRG-1 / 15-oxoprostaglandin 13-reductase / Dithiolethione-inducible gene 1 protein / D3T-inducible ...

Mass: 35968.734 Da / Num. of mol.: 4 / Fragment: T4-A329 / Mutation: A27S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: PTGR1, LTB4DH / Plasmid: HosaA.00871.a.A2 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q14914, 13,14-dehydro-15-oxoprostaglandin 13-reductase, 2-alkenal reductase [NAD(P)+]

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Non-polymers , 5 types, 463 molecules

#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-IMN / INDOMETHACIN Mass: 357.788 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₉H₁₆ClNO₄ / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.43 Å³/Da / Density % sol: 49.37 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Berkeley C9: 25% (w/v) PEG 3350, 100 mM Bis-Tris pH 6.5, 100 mM sodium acetate. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag cleaved with 3C protease. 2mM NADP+ and 2mM indomethacin ...Details: Berkeley C9: 25% (w/v) PEG 3350, 100 mM Bis-Tris pH 6.5, 100 mM sodium acetate. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag cleaved with 3C protease. 2mM NADP+ and 2mM indomethacin addied prior to crystallization, plate 14493 well C9 drop 2 , Puck: PSL1906, Cryo: 50% crystallant + 50% PEG 3350 (37.5% PEG 3350 total).

Crystal

Density Matthews: 2.43 Å³/Da / Density % sol: 49.37 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Berkeley C9: 25% (w/v) PEG 3350, 100 mM Bis-Tris pH 6.5, 100 mM sodium acetate. HosaA.00871.a.A2.PW39298 at 16.1 mg/mL. His tag cleaved with 3C protease. 2mM NADP+ and 2mM indomethacin ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 24, 2024
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.1→49.59 Å / Num. obs: 80333 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC_1/2: 0.991 / R_merge(I) obs: 0.202 / R_pim(I) all: 0.09 / R_rim(I) all: 0.222 / Χ²: 0.99 / Net I/σ(I): 8.7 / Num. measured all: 488196
Reflection shell	Resolution: 2.1→2.14 Å / % possible obs: 99.9 % / Redundancy: 6.3 % / R_merge(I) obs: 1.323 / Num. measured all: 28931 / Num. unique obs: 4594 / CC_1/2: 0.533 / R_pim(I) all: 0.574 / R_rim(I) all: 1.444 / Χ²: 1.01 / Net I/σ(I) obs: 2.1

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Processing

Software

Name	Version	Classification
PHENIX	dev_5493	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→47.36 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.21 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2362	3922	4.88 %
R_work	0.1998	-	-
obs	0.2016	80287	99.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.1→47.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10008	0	302	453	10763

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	10540
X-RAY DIFFRACTION	f_angle_d	0.557	14317
X-RAY DIFFRACTION	f_dihedral_angle_d	13.362	4047
X-RAY DIFFRACTION	f_chiral_restr	0.042	1600
X-RAY DIFFRACTION	f_plane_restr	0.008	1778

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.1-2.13	0.3071	149	0.284	2734	X-RAY DIFFRACTION	100
2.13-2.15	0.3025	111	0.2539	2747	X-RAY DIFFRACTION	100
2.15-2.18	0.2672	141	0.2553	2707	X-RAY DIFFRACTION	100
2.18-2.21	0.2975	140	0.2451	2704	X-RAY DIFFRACTION	100
2.21-2.24	0.2627	136	0.244	2744	X-RAY DIFFRACTION	100
2.24-2.28	0.2869	127	0.2373	2701	X-RAY DIFFRACTION	100
2.28-2.31	0.2569	147	0.2351	2729	X-RAY DIFFRACTION	100
2.31-2.35	0.2495	137	0.2351	2701	X-RAY DIFFRACTION	100
2.35-2.39	0.2725	142	0.2361	2707	X-RAY DIFFRACTION	100
2.39-2.43	0.3119	140	0.2302	2761	X-RAY DIFFRACTION	100
2.43-2.48	0.2965	127	0.2352	2701	X-RAY DIFFRACTION	100
2.48-2.53	0.2726	145	0.2372	2721	X-RAY DIFFRACTION	100
2.53-2.59	0.3137	146	0.2409	2728	X-RAY DIFFRACTION	100
2.59-2.65	0.2853	117	0.2424	2745	X-RAY DIFFRACTION	100
2.65-2.71	0.3013	151	0.2384	2696	X-RAY DIFFRACTION	100
2.71-2.79	0.2811	166	0.2295	2695	X-RAY DIFFRACTION	100
2.79-2.87	0.2373	148	0.2195	2698	X-RAY DIFFRACTION	100
2.87-2.96	0.2824	133	0.2171	2759	X-RAY DIFFRACTION	100
2.96-3.07	0.268	132	0.2157	2716	X-RAY DIFFRACTION	100
3.07-3.19	0.2382	130	0.2166	2736	X-RAY DIFFRACTION	100
3.19-3.33	0.258	123	0.2113	2738	X-RAY DIFFRACTION	100
3.33-3.51	0.22	124	0.2027	2767	X-RAY DIFFRACTION	100
3.51-3.73	0.2083	160	0.1768	2701	X-RAY DIFFRACTION	100
3.73-4.02	0.1919	168	0.1676	2707	X-RAY DIFFRACTION	100
4.02-4.42	0.1936	140	0.1516	2759	X-RAY DIFFRACTION	100
4.42-5.06	0.1797	140	0.1442	2734	X-RAY DIFFRACTION	99
5.06-6.37	0.2183	154	0.1673	2733	X-RAY DIFFRACTION	100
6.37-47.36	0.1912	148	0.1668	2796	X-RAY DIFFRACTION	99

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	2.266	0.0632	0.4125	1.1099	0.9118	2.6068	0.0081	-0.1418	-0.3369	0.1082	0.1151	-0.0503	0.3601	-0.0519	-0.1356	0.2952	-0.0049	-0.0005	0.2311	0.0449	0.2738	34.0683	-24.6985	35.1195
2	0.6518	-0.5847	-0.0311	0.8895	-0.2874	2.5269	0.0845	-0.0016	0.0901	0.0533	0.072	-0.0967	-0.3493	0.5161	-0.081	0.2241	-0.0812	0.0092	0.2922	-0.0497	0.2257	43.3457	-7.9602	32.0826
3	0.7034	0.0542	-0.4581	0.498	-0.425	2.72	0.0812	0.0109	0.084	-0.0081	0.0352	0.0506	-0.4187	-0.0759	-0.098	0.2547	0.0073	0.0325	0.171	-0.0127	0.214	32.3071	-3.9391	18.5057
4	1.6463	0.8107	-0.5132	1.1302	-0.6407	2.2817	0.0092	0.0927	0.1701	-0.0084	0.0955	0.0906	-0.3598	-0.1065	-0.1015	0.282	-0.0104	-0.0184	0.2098	-0.0138	0.2315	34.7793	-1.0984	-28.9226
5	0.7902	-0.1927	-0.3475	2.3224	-0.2643	1.8946	-0.0379	-0.0277	-0.0365	0.1017	0.0881	-0.1083	0.0708	0.2239	-0.0421	0.2211	0.0063	-0.0327	0.2242	-0.0255	0.186	47.0851	-21.3747	-10.0123
6	0.7057	0.0526	-0.0481	0.9367	0.1114	2.0376	-0.053	0.006	0.0457	0.021	0.044	0.0662	0.0823	0.0442	0.0098	0.1925	-0.0073	0.0041	0.1782	-0.0158	0.1935	41.3972	-14.3111	-11.2021
7	1.5771	0.51	0.1543	1.5087	0.847	2.0126	-0.0567	0.0706	-0.2306	-0.0655	0.102	-0.265	0.1972	0.0231	-0.0557	0.3007	-0.0615	0.0192	0.2699	-0.0001	0.287	14.2798	-40.6902	-28.4133
8	1.1974	-0.219	-0.6002	2.4336	0.4018	1.8894	-0.0779	0.0014	0.037	0.2524	0.0282	0.0683	-0.0658	-0.4247	0.0603	0.2368	0.026	-0.0046	0.3294	0.0266	0.2332	-4.0693	-23.6989	-13.0563
9	0.7525	0.1867	-0.7612	1.2273	0.1394	2.818	-0.1252	0.0203	-0.1077	0.0336	0.0109	0.0503	0.0067	-0.2238	0.0963	0.2136	0.0113	-0.043	0.2665	0.0288	0.2159	2.1955	-28.8796	-11.2403
10	2.3181	0.8177	-0.4797	1.9767	0.2943	2.0826	0.0599	-0.231	0.2341	0.1747	-0.0946	0.2297	-0.1956	-0.4768	-0.0392	0.2637	0.0462	0.0094	0.3196	-0.0165	0.2213	-3.0669	-21.0316	35.6483
11	0.5615	-0.0811	-0.0842	1.3664	-0.1244	2.0824	0.0072	0.0459	-0.0315	-0.1258	-0.0792	0.0007	0.3704	-0.2225	0.0719	0.2639	-0.0539	0	0.2432	0.0113	0.2117	5.6337	-38.9283	20.7634

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 66 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 67 through 164 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 165 through 329 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 112 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 113 through 219 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 220 through 329 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 112 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 113 through 206 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 207 through 329 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 2 through 93 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 94 through 329 )

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