PDB-7ulx: Human DDAH1 soaked with its inhibitor N4-(4-chloropyridin-2-yl)-L...

ID or keywords:

Entry

Database: PDB / ID: 7ulx

Title

Human DDAH1 soaked with its inhibitor N4-(4-chloropyridin-2-yl)-L-asparagine

Components

N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

Keywords

HYDROLASE / DDAH1 / Dimethylargininase / DDAH / inhibitor / N4-(4-chloropyridin-2-yl)-L-asparagine

Function / homology

Function and homology information

dimethylargininase / dimethylargininase activity / citrulline metabolic process / negative regulation of cellular response to hypoxia / arginine metabolic process / regulation of systemic arterial blood pressure / negative regulation of vascular permeability / amino acid binding / catalytic activity / nitric oxide mediated signal transduction ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.707 Å

Authors

Zheng, Y. / Butrin, A. / Tuley, A. / Liu, D. / Fast, W.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Optimization of a switchable electrophile fragment into a potent and selective covalent inhibitor of human DDAH1
Authors: Tuley, A. / Zheng, Y. / Tommasi, S. / Butrin, A. / May, K.V. / Ahn, Y. / Reidl, T.C. / Weerakoon, L. / Hulin, J. / Meech, R. / Patel, D.S. / Horton, C.P. / Swartzel, C.J. / Kim, Y. / ...

History

Deposition	Apr 5, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 30, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ulx.cif.gz	240.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7ulx.ent.gz	190.9 KB	Display	PDB format
PDBx/mmJSON format	7ulx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ul/7ulx ftp://data.pdbj.org/pub/pdb/validation_reports/ul/7ulx	HTTPS FTP

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Related structure data

Related structure data	7uluC 7ulvC 3p8eS S: Starting model for refinement C: citing same article (ref.)
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	#44 - Aug 2003 Calmodulin similarity (1) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #206 - Feb 2017 Globin Evolution similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1)

Deposited unit

A: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

B: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

hetero molecules

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

1

A: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

hetero molecules

defined by author
Evidence: gel filtration
33.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	73.435, 47.590, 81.120
Angle α, β, γ (deg.)	90.000, 109.010, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 / Dimethylarginine dimethylaminohydrolase 1 / DDAHI / Dimethylargininase-1 Mass: 33623.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDAH1, DDAH / Production host: Escherichia coli (E. coli) / References: UniProt: O94760, dimethylargininase
#2: Chemical	ChemComp-NQ6 / N-(pyridin-2-yl)-L-asparagine Mass: 209.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₁N₃O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.99 Å³/Da / Density % sol: 38.28 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Purified DDAH1 was concentrated to approximately 10 mg/mL using an Amicon-Ultra centrifugal filter device (10 kDa MWCO). The protein was crystallized at 25 C using the hanging drop method ...Details: Purified DDAH1 was concentrated to approximately 10 mg/mL using an Amicon-Ultra centrifugal filter device (10 kDa MWCO). The protein was crystallized at 25 C using the hanging drop method (Hampton Research, Aliso Viejo, CA) from 25 % (w/v) PEG6000, 0.1 M Tris-HCl, pH 8.2. Further optimization was done manually using a 1:1 well solution : DDAH1 stock solution ratio to improve crystal size and morphology. Crystals grew to their maximum size in 3 weeks and were harvested after approximately 25 days. To determine the structure of DDAH1 in complex with the ligand, the crystals were transferred to a reservoir containing 20 uL of 20 mM of the ligand in the crystallization mother liquor (25% PEG 6000, 0.1 M Tris-HCl, pH 8.2) and soaked for 30 min. Before data collection, crystals with good size and morphology were transferred into a cryoprotection solution (Well Solution supplemented with 25 % (v/v) glycerol) for 1 to 5 seconds using a the cryoloop (Hampton Research, Laguna Niguel, CA). Individual hDDAH1:ligand crystals were flash frozen in liquid nitrogen before use.

Crystal

Density Matthews: 1.99 Å³/Da / Density % sol: 38.28 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, hanging drop
Details: Purified DDAH1 was concentrated to approximately 10 mg/mL using an Amicon-Ultra centrifugal filter device (10 kDa MWCO). The protein was crystallized at 25 C using the hanging drop method ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.9787 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9787 Å / Relative weight: 1

Reflection

Resolution: 1.707→50 Å / Num. obs: 56084 / % possible obs: 96.9 % / Redundancy: 3.7 % / R_merge(I) obs: 0.067 / R_pim(I) all: 0.04 / R_rim(I) all: 0.078 / Χ²: 0.9 / Net I/σ(I): 7.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.71-1.74	2.8	0.642	2513	0.624	0.42	0.772	0.813	88.5
1.74-1.77	3	0.573	2748	0.723	0.37	0.686	0.782	94.5
1.77-1.81	3.3	0.573	2799	0.739	0.358	0.68	0.841	98.3
1.81-1.84	3.7	0.493	2879	0.871	0.289	0.574	0.812	99.8
1.84-1.88	3.9	0.416	2871	0.888	0.239	0.481	0.858	99.9
1.88-1.93	4	0.35	2875	0.93	0.201	0.405	0.903	100
1.93-1.97	4	0.273	2864	0.955	0.155	0.315	0.969	100
1.97-2.03	4	0.226	2864	0.962	0.128	0.261	0.961	100
2.03-2.09	4	0.187	2922	0.972	0.106	0.216	0.995	99.8
2.09-2.15	4	0.156	2841	0.979	0.089	0.18	0.99	99.9
2.15-2.23	4	0.121	2878	0.989	0.069	0.139	0.972	99.9
2.23-2.32	4	0.109	2885	0.987	0.062	0.125	0.987	99.9
2.32-2.43	4	0.091	2900	0.992	0.052	0.105	0.968	99.9
2.43-2.55	3.9	0.076	2884	0.994	0.044	0.088	0.912	99.8
2.55-2.71	3.9	0.068	2856	0.993	0.039	0.079	0.902	99.7
2.71-2.92	3.8	0.057	2922	0.995	0.034	0.067	0.816	99.5
2.92-3.22	3.7	0.05	2853	0.995	0.03	0.058	0.82	98.6
3.22-3.68	3.5	0.046	2764	0.994	0.029	0.055	0.812	94.4
3.68-4.64	3.3	0.044	2508	0.994	0.028	0.052	0.821	85.5
4.64-50	3.3	0.046	2458	0.993	0.029	0.055	0.904	81.2

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Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX	1.14_3260	refinement
PDB_EXTRACT	3.27	data extraction
iMOSFLM		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3P8E

3p8e

Resolution: 1.707→28.348 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2351	2322	4.9 %
R_work	0.1913	45024	-
obs	0.1934	47346	81.69 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 89.82 Å² / B_iso mean: 27.7625 Å² / B_iso min: 3.01 Å²

Refinement step

Cycle: final / Resolution: 1.707→28.348 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4236	0	0	537	4773
B_iso mean	-	-	-	34.1	-
Num. residues	-	-	-	-	550

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.707-1.7416	0.3294	66	0.22	1188	37
1.7416-1.7795	0.2268	74	0.2256	1470	46
1.7795-1.8209	0.2357	77	0.232	1795	55
1.8209-1.8664	0.2449	101	0.2323	2013	63
1.8664-1.9169	0.2891	111	0.2343	2248	70
1.9169-1.9732	0.2534	140	0.2196	2484	77
1.9732-2.0369	0.2669	149	0.2094	2731	84
2.0369-2.1097	0.2515	136	0.199	2978	93
2.1097-2.1941	0.25	162	0.1922	3193	98
2.1941-2.294	0.1956	167	0.1938	3223	100
2.294-2.4148	0.2381	159	0.1945	3235	100
2.4148-2.566	0.2638	181	0.1942	3207	100
2.566-2.764	0.255	154	0.2024	3255	100
2.764-3.0419	0.2464	173	0.2044	3222	99
3.0419-3.4814	0.2411	163	0.1815	3171	97
3.4814-4.3835	0.2079	174	0.1578	2853	88
4.3835-28.348	0.1952	135	0.1696	2758	82

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	0.5449	-0.1929	0.1119	0.9368	-0.1353	1.0734	-0.0107	0.0275	-0.0498	0.1333	-0.0247	0.0231	0.0006	0.0242	-0.0032	0.0813	0.0088	-0.0167	0.0453	-0.0003	0.121	-0.7396	-2.6164	44.2995
2	1.1526	-0.0498	-0.1069	0.9888	0.2385	0.6248	0.0116	0.1078	0.008	-0.0094	0.0048	0.1347	-0.0198	-0.1601	-0.0193	0.0857	-0.0325	-0.004	0.0115	-0.003	0.1017	-9.6213	-5.4767	37.6674
3	0.7562	-0.7844	0.3391	1.293	-0.3025	0.6527	-0.0689	-0.1858	-0.1433	0.3371	0.0446	0.0054	0.0902	-0.1219	0.0334	0.1189	0.0133	-0.0212	0.0558	0.0186	0.0941	-3.3666	-3.4957	47.4361
4	1.103	0.273	-0.1161	0.7722	0.2154	1.0184	-0.0297	-0.1067	0.0417	0.162	0.0256	-0.1968	0.0278	0.1812	0.0122	0.0515	-0.0098	-0.0717	0.0638	0.0013	0.0658	6.8432	7.1625	45.8988
5	1.5085	-0.8977	0.7694	1.7564	-1.1793	1.4111	-0.0671	-0.3374	0.0935	0.415	0.0849	0.0112	-0.0441	-0.0347	0.0969	0.2399	0.0128	-0.059	0.139	-0.054	0.0727	-0.4757	7.1697	51.9854
6	0.6644	-0.073	0.1484	0.7052	-0.1681	0.6835	-0.0661	-0.103	0.1284	0.194	0.1199	-0.1765	-0.1026	0.1162	-0.0048	0.1203	0.0033	-0.0456	0.0728	-0.035	0.1078	7.6077	10.9947	46.2292
7	0.6579	-0.177	-0.0415	0.819	0.1938	0.6523	0.0655	0.0281	0.1026	-0.063	0.0862	-0.297	-0.3349	0.2162	0.0996	0.1346	-0.1169	0.0059	0.1242	-0.0529	0.1627	12.8687	12.4694	37.9464
8	0.8293	0.2094	-0.123	1.1981	0.1684	1.0937	-0.1283	0.1855	-0.1193	-0.255	0.1392	-0.3129	-0.1451	0.2678	0.0387	0.083	-0.0409	0.0178	0.1436	-0.0371	0.1158	10.8109	-0.5089	28.8184
9	0.4262	0.1248	0.2436	0.4442	0.3809	0.9487	0.0006	0.1872	-0.1458	-0.1216	0.0301	-0.0165	0.2112	-0.0295	-0.0484	0.1892	-0.0723	-0.0013	0.2237	-0.1576	0.0771	1.5644	-11.2826	24.0872
10	1.2463	0.0214	0.13	0.7982	0.1283	0.818	-0.0576	0.097	-0.1305	-0.0021	0.0677	-0.1664	0.1034	0.0567	0.0079	0.0667	0.0074	-0.003	0.0565	-0.0126	0.0965	2.6205	-6.0016	36.5279
11	0.9202	-0.2754	0.0518	1.1053	0.565	0.7846	0.1005	-0.123	0.0049	0.4591	0.0359	-0.002	-0.0406	-0.2247	-0.0853	0.2929	0.0121	0.0502	0.2762	0.0767	0.2189	-12.1331	8.7146	6.9591
12	1.5529	0.1136	0.1755	1.5394	-0.458	0.2472	0.0745	0.0032	-0.0812	0.2131	0.0163	-0.3059	-0.1154	0.0536	-0.0719	0.2271	-0.0055	-0.0489	0.2046	0.0081	0.2715	-4.185	12.1124	0.203
13	0.9252	-0.6928	0.1006	1.3003	-0.176	0.7123	0.0396	-0.2478	0.1391	0.4225	0.096	-0.0297	-0.0842	0.0567	-0.077	0.3677	-0.0219	-0.0362	0.2848	0.062	0.1904	-8.8474	8.6756	9.7362
14	0.6614	0.1495	-0.12	0.6091	-0.4241	0.7901	0.018	-0.1259	-0.079	0.2256	0.0717	0.1868	-0.1118	-0.1644	0.0666	0.2919	0.0331	0.11	0.3205	0.1598	0.2897	-19.5152	-1.1	8.9122
15	0.5695	-0.8608	-0.7034	1.3515	1.1233	0.9357	0.0242	-0.342	-0.1212	0.5843	0.1421	0.1287	0.0069	0.0015	-0.0118	0.5484	0.0417	0.0372	0.4025	0.1234	0.2714	-11.6596	-1.1027	14.2766
16	0.6136	-0.0892	-0.0584	0.5158	0.235	0.7436	0.0439	-0.1762	-0.16	0.4025	0.0809	0.1252	0.025	-0.0736	0.0193	0.3455	0.0042	0.0995	0.3347	0.1538	0.3165	-20.2769	-4.9907	9.1845
17	1.7695	-0.3508	-0.0594	1.3334	0.1074	1.1881	0.1173	0.1113	-0.0077	-0.1993	0.083	0.0952	0.0892	-0.1787	-0.0768	0.2094	-0.0777	0.0034	0.4121	0.091	0.5	-23.5341	-3.9466	-1.9023
18	0.4852	0.4085	0.0177	0.8675	-0.4452	0.4066	-0.0801	0.0348	-0.3847	0.1251	0.1089	0.2492	0.1778	-0.1814	0.0525	0.2788	-0.0993	0.0664	0.3765	0.1035	0.4068	-24.2532	-3.9053	-0.707
19	0.278	0.004	0.2417	1.8912	0.262	1.1693	0.0656	0.2628	-0.2686	-0.1251	0.0448	0.1006	0.2988	-0.137	-0.0054	0.3227	-0.1791	-0.1877	0.5968	0.1145	0.5032	-26.4698	1.7401	-12.5913
20	1.4736	0.2535	-0.0942	0.7949	-0.0554	1.1291	-0.0106	0.1366	0.0313	-0.161	0.0962	0.5071	-0.0926	-0.3238	-0.0297	0.2205	0.0298	-0.0072	0.4066	0.1452	0.3042	-26.228	10.988	-5.7461
21	0.5734	0.1146	-0.5181	0.1255	-0.2066	0.9413	0.0152	0.1123	0.109	-0.0393	0.0626	0.0987	-0.105	-0.0797	-0.1002	0.2139	0.0773	0.1689	0.4361	0.2795	0.2308	-17.7642	18.2462	-9.6185
22	0.8697	-0.0857	-0.1721	0.7373	0.2086	0.5629	0.0225	0.0519	0.055	0.2332	0.0655	0.1521	-0.1097	-0.173	-0.0347	0.1961	0.0508	0.0783	0.2827	0.0846	0.1918	-16.0895	12.2684	-0.3269

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 28 )	A	8 - 28
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 29 through 55 )	A	29 - 55
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 56 through 76 )	A	56 - 76
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 77 through 95 )	A	77 - 95
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 96 through 111 )	A	96 - 111
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 112 through 133 )	A	112 - 133
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 134 through 167 )	A	134 - 167
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 168 through 236 )	A	168 - 236
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 237 through 251 )	A	237 - 251
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 252 through 282 )	A	252 - 282
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 8 through 28 )	B	8 - 28
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 29 through 56 )	B	29 - 56
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 57 through 76 )	B	57 - 76
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 77 through 95 )	B	77 - 95
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 96 through 111 )	B	96 - 111
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 112 through 133 )	B	112 - 133
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 134 through 147 )	B	134 - 147
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 148 through 182 )	B	148 - 182
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 183 through 204 )	B	183 - 204
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 205 through 230 )	B	205 - 230
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 231 through 251 )	B	231 - 251
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 252 through 282 )	B	252 - 282

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-Basic information

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-Download

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+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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi