PDB-9d6x: Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in c...

ID or keywords:

Entry

Database: PDB / ID: 9d6x

Title

Crystal structure of Human Prostaglandin reductase 1 (PTGR1) in complex with methotrexate (Monoclinic P form)

Components

Prostaglandin reductase 1

Keywords

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

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: 1.95 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 methotrexate (Monoclinic P form)
Authors: Lovell, S. / Enayati, P. / Cooper, A. / Liu, L. / Battaile, K.P.

History

Deposition	Aug 16, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 20, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9d6x.cif.gz	518.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9d6x.ent.gz	425.7 KB	Display	PDB format
PDBx/mmJSON format	9d6x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9d6x_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	9d6x_full_validation.pdf.gz	1.3 MB	Display
Data in XML	9d6x_validation.xml.gz	56.5 KB	Display
Data in CIF	9d6x_validation.cif.gz	74.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d6/9d6x ftp://data.pdbj.org/pub/pdb/validation_reports/d6/9d6x	HTTPS FTP

-
Related structure data

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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#13 - Jan 2001 Alcohol Dehydrogenase similarity (5) #34 - Oct 2002 Dihydrofolate Reductase similarity (1) #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

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

1

A: Prostaglandin reductase 1

B: Prostaglandin reductase 1

hetero molecules

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

2

C: Prostaglandin reductase 1

D: Prostaglandin reductase 1

hetero molecules

defined by author&software
76.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	90.273, 83.863, 98.674
Angle α, β, γ (deg.)	90.00, 90.34, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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: 37959.938 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)+]
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-MTX / METHOTREXATE Mass: 454.439 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₀H₂₂N₈O₅ / Feature type: SUBJECT OF INVESTIGATION / Comment: chemotherapy*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 50 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Berkeley A12: 35% (w/v) PEG 3350, 100 mM Hepes free acid/ Sodium hydroxide pH 7.5, 10% (v/v) 2-Propanol. HosaA.00871.a.A2.PW39293 at 24.7 mg/mL. 2mM methotrexate added to the protein prior ...Details: Berkeley A12: 35% (w/v) PEG 3350, 100 mM Hepes free acid/ Sodium hydroxide pH 7.5, 10% (v/v) 2-Propanol. HosaA.00871.a.A2.PW39293 at 24.7 mg/mL. 2mM methotrexate added to the protein prior to crystallization. Plate 14259 well A12 drop 2, Puck: PSL0103, Cryo: Direct.

Crystal

Density Matthews: 2.46 Å³/Da / Density % sol: 50 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Berkeley A12: 35% (w/v) PEG 3350, 100 mM Hepes free acid/ Sodium hydroxide pH 7.5, 10% (v/v) 2-Propanol. HosaA.00871.a.A2.PW39293 at 24.7 mg/mL. 2mM methotrexate added to the protein prior ...

-
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: Aug 4, 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: 1.95→45.14 Å / Num. obs: 105715 / % possible obs: 98.7 % / Redundancy: 6.9 % / CC_1/2: 0.995 / R_merge(I) obs: 0.115 / R_pim(I) all: 0.048 / R_rim(I) all: 0.125 / Χ²: 1.1 / Net I/σ(I): 9.6 / Num. measured all: 727429
Reflection shell	Resolution: 1.95→1.98 Å / % possible obs: 97.9 % / Redundancy: 6.7 % / R_merge(I) obs: 1.07 / Num. measured all: 34597 / Num. unique obs: 5140 / CC_1/2: 0.742 / R_pim(I) all: 0.445 / R_rim(I) all: 1.16 / Χ²: 1.05 / Net I/σ(I) obs: 1.9

-
Processing

Software

Name	Version	Classification
PHENIX	dev_5421	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→45.14 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2158	5277	4.99 %
R_work	0.1837	-	-
obs	0.1853	105675	98.47 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→45.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10008	0	135	507	10650

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	10374
X-RAY DIFFRACTION	f_angle_d	0.721	14050
X-RAY DIFFRACTION	f_dihedral_angle_d	13.531	3896
X-RAY DIFFRACTION	f_chiral_restr	0.046	1574
X-RAY DIFFRACTION	f_plane_restr	0.006	1820

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 (%)
1.95-1.97	0.2782	177	0.2711	3274	X-RAY DIFFRACTION	98
1.97-2	0.3223	165	0.2618	3322	X-RAY DIFFRACTION	98
2-2.02	0.285	170	0.2374	3337	X-RAY DIFFRACTION	98
2.02-2.05	0.2746	197	0.2266	3271	X-RAY DIFFRACTION	98
2.05-2.07	0.2668	170	0.2287	3268	X-RAY DIFFRACTION	98
2.07-2.1	0.2977	190	0.227	3363	X-RAY DIFFRACTION	98
2.1-2.13	0.2432	182	0.2227	3264	X-RAY DIFFRACTION	98
2.13-2.16	0.2518	190	0.2072	3331	X-RAY DIFFRACTION	98
2.16-2.2	0.2221	153	0.1987	3359	X-RAY DIFFRACTION	98
2.2-2.23	0.2375	208	0.1909	3263	X-RAY DIFFRACTION	98
2.23-2.27	0.2516	174	0.1941	3334	X-RAY DIFFRACTION	98
2.27-2.31	0.2609	163	0.198	3330	X-RAY DIFFRACTION	98
2.31-2.36	0.2209	174	0.1886	3339	X-RAY DIFFRACTION	99
2.36-2.4	0.2417	182	0.1786	3330	X-RAY DIFFRACTION	98
2.4-2.46	0.2081	162	0.1806	3365	X-RAY DIFFRACTION	99
2.46-2.51	0.2405	178	0.1817	3331	X-RAY DIFFRACTION	99
2.51-2.58	0.2618	199	0.1873	3327	X-RAY DIFFRACTION	99
2.58-2.65	0.2323	176	0.191	3364	X-RAY DIFFRACTION	99
2.65-2.72	0.2529	122	0.2016	3400	X-RAY DIFFRACTION	99
2.72-2.81	0.2442	179	0.2025	3371	X-RAY DIFFRACTION	99
2.81-2.91	0.2095	153	0.1926	3385	X-RAY DIFFRACTION	99
2.91-3.03	0.2088	236	0.1931	3304	X-RAY DIFFRACTION	99
3.03-3.17	0.255	184	0.1928	3364	X-RAY DIFFRACTION	99
3.17-3.33	0.2252	210	0.2004	3351	X-RAY DIFFRACTION	99
3.33-3.54	0.2183	123	0.1859	3390	X-RAY DIFFRACTION	99
3.54-3.82	0.2199	228	0.1681	3328	X-RAY DIFFRACTION	98
3.82-4.2	0.1634	175	0.1543	3322	X-RAY DIFFRACTION	98
4.2-4.81	0.1472	135	0.1446	3457	X-RAY DIFFRACTION	99
4.81-6.05	0.176	151	0.1689	3468	X-RAY DIFFRACTION	100
6.05-45.14	0.1976	171	0.1824	3486	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	3.7893	1.2268	0.7989	3.6834	1.2637	1.8321	-0.0795	0.5568	0.4074	-0.4469	-0.0307	-0.0263	-0.2847	0.1041	0.0963	0.2854	0.001	0.0253	0.4538	0.0806	0.2812	-9.0009	9.1696	-20.2813
2	3.0706	-0.2929	0.9575	0.9385	-0.2063	1.2205	0.0326	0.0624	-0.1884	-0.0673	0.0198	0.069	0.0772	0.0056	-0.0463	0.2336	0.0042	0.0145	0.2247	-0.0105	0.2062	-32.1749	-0.6644	-4.8305
3	3.2178	-1.0564	-0.9789	3.0413	3.0578	5.9011	-0.0925	0.1891	-0.0155	-0.0043	0.0661	-0.0751	0.1339	0.4222	0.0254	0.2261	-0.0286	-0.0058	0.3081	0.0042	0.2152	-14.1619	2.8594	-6.4451
4	3.8035	-1.036	-1.2894	3.4719	1.5127	2.4755	-0.1453	-0.2448	-0.2772	0.5055	0.0496	0.0617	0.2766	-0.0558	0.098	0.2672	-0.0196	-0.0095	0.2473	0.0092	0.2898	-75.351	-0.0824	-6.3864
5	2.6303	-0.1754	0.0199	1.1328	-0.3008	1.3673	0.0031	0.5363	0.1893	-0.0739	-0.0872	-0.0653	-0.0443	0.1327	0.0834	0.233	-0.005	-0.0192	0.3463	0.0359	0.223	-53.9721	12.5679	-23.4819
6	3.9588	-0.0264	0.698	0.8312	0.114	1.0216	0.0196	0.1289	0.0339	0.1206	-0.0644	0.0956	-0.0463	-0.0126	0.0425	0.294	0.0034	0.0125	0.2635	0.0188	0.2226	-60.8298	8.048	-16.6635
7	2.6243	0.6272	0.6896	4.2528	1.6096	2.5935	-0.0785	0.3858	0.0726	-0.6743	0.0496	0.0959	-0.2348	-0.099	0.0176	0.2913	-0.0037	0.0208	0.3827	-0.0135	0.2923	-73.0972	-23.8416	-42.8831
8	6.0083	-0.2376	2.1312	1.643	-1.0591	3.2036	-0.0089	0.0566	-0.365	0.0228	-0.0791	0.0813	0.1208	0.0627	0.0962	0.2666	-0.0512	0.0406	0.2682	-0.0835	0.2749	-56.8966	-39.9943	-32.4368
9	3.7834	0.1989	-1.3907	0.8065	-0.4252	1.7198	0.0703	-0.2709	-0.0366	0.0405	-0.0813	0.0097	-0.0399	0.1813	0.0124	0.2572	-0.0408	0.0161	0.2865	-0.0244	0.2182	-47.11	-32.6443	-25.4428
10	3.7783	-0.9563	-0.3814	5.2934	0.5734	1.5075	-0.0387	0.1605	-0.1461	-0.0435	-0.0333	0.2991	0.0593	-0.1697	0.0814	0.2424	-0.058	0.0085	0.2889	-0.0587	0.2905	-67.7772	-34.2988	-32.0164
11	3.3655	-1.0678	-0.8701	3.6238	1.5357	2.2391	-0.1778	-0.5554	-0.3996	0.3898	0.0258	-0.0298	0.1977	0.1117	0.1572	0.2421	-0.0296	-0.0008	0.483	0.0827	0.3078	-6.3633	-33.1802	-28.8132
12	4.5318	-0.1285	-0.3531	1.0585	0.2162	1.5377	0.0596	0.3127	0.4556	-0.0302	0.0055	-0.0048	-0.0748	-0.0785	-0.0667	0.2263	-0.0405	0.0023	0.3111	0.0358	0.2311	-28.6467	-22.0246	-45.1788
13	4.0009	0.9783	-0.0996	0.7415	0.0289	0.5933	-0.0136	0.1139	-0.1315	0.0365	0.0567	-0.1293	-0.0067	0.0302	-0.0522	0.2705	0.0066	-0.0107	0.3469	-0.0004	0.2014	-19.5243	-28.2149	-41.6652

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 112 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 113 through 277 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 278 through 329 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 112 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 113 through 245 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 246 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 164 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 165 through 276 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 277 through 329 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 2 through 112 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 113 through 256 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 257 through 329 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi