PDB-6oia: (1S,3S)-3-amino-4-(perfluoropropan-2-ylidene)cyclopentane-1-carbo...

ID or keywords:

Entry

Database: PDB / ID: 6oia

Title

(1S,3S)-3-amino-4-(perfluoropropan-2-ylidene)cyclopentane-1-carboxylic acid hydrochloride, a potent inhibitor of ornithine aminotransferase

Components

Ornithine aminotransferase, mitochondrial

Keywords

TRANSFERASE / Human Ornithine Aminotransferase (hOAT) Mechanism Based Inhibitors Hepatocellular Carcinoma PLP

Function / homology

Function and homology information

arginine catabolic process to proline via ornithine /

ornithine aminotransferase activity /

ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism /

visual perception /

pyridoxal phosphate binding /

mitochondrial matrix /

mitochondrion ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.777 Å

Authors

Catlin, D.S. / Liu, D. / Moschitto, M.J. / Doubleday, P.F. / Kelleher, N. / Silverman, R.B.

Funding support

United States, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2019
Title: Mechanism of Inactivation of Ornithine Aminotransferase by (1S,3S)-3-Amino-4-(hexafluoropropan-2-ylidenyl)cyclopentane-1-carboxylic Acid.
Authors: Moschitto, M.J. / Doubleday, P.F. / Catlin, D.S. / Kelleher, N.L. / Liu, D. / Silverman, R.B.

History

Deposition	Apr 9, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 18, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2	Apr 1, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6oia.cif.gz	499.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6oia.ent.gz	424.2 KB	Display	PDB format
PDBx/mmJSON format	6oia.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/oi/6oia ftp://data.pdbj.org/pub/pdb/validation_reports/oi/6oia	HTTPS FTP

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Related structure data

Similar structure data	6v8c-2 7jx9-2 2can-2 6v8d-2 4jey-d 1oat-1 6v8c-1 4jex-d 2can-1 4dqp-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Ornithine aminotransferase, mitochondrial

B: Ornithine aminotransferase, mitochondrial

C: Ornithine aminotransferase, mitochondrial

hetero molecules

136 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ornithine aminotransferase, mitochondrial

B: Ornithine aminotransferase, mitochondrial

hetero molecules

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

2

C: Ornithine aminotransferase, mitochondrial

hetero molecules

C: Ornithine aminotransferase, mitochondrial

hetero molecules

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

Unit cell

Length a, b, c (Å)	115.824, 115.824, 187.644
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	C-726- HOH
2	1	C-941- HOH

#1: Protein	Ornithine aminotransferase, mitochondrial / / Ornithine delta-aminotransferase / Ornithine--oxo-acid aminotransferase Mass: 44860.320 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OAT / Production host: Escherichia coli (E. coli) / References: UniProt: P04181, ornithine aminotransferase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-MQ4 / (1S)-3-amino-4-[(2S)-1,1,1-trifluoro-3-oxopropan-2-yl]cyclopent-3-ene-1-carboxylic acid Mass: 237.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₀F₃NO₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1079 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 54.44 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 6000, 200 mM NaCl, 2.5 % Glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 21, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.75→50 Å / Num. obs: 125931 / % possible obs: 89.78 % / Redundancy: 10.9 % / B_iso Wilson estimate: 19.52 Å² / Net I/σ(I): 1.37
Reflection shell	Resolution: 1.75→1.78 Å / Num. unique obs: 7324

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Processing

Software

Name	Version	Classification
SCALA		data scaling
PHENIX	1.11.1_2575	refinement
PDB_EXTRACT	3.24	data extraction
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.777→29.487 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.93

	R_factor	Num. reflection	% reflection
R_free	0.1891	6318	5.02 %
R_work	0.1614	-	-
obs	0.1628	125923	89.78 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 117.89 Å² / B_iso mean: 29.082 Å² / B_iso min: 7.01 Å²

Refinement step

Cycle: final / Resolution: 1.777→29.487 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9483	0	89	1079	10651
B_iso mean	-	-	33.65	37.91	-
Num. residues	-	-	-	-	1212

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	9943
X-RAY DIFFRACTION	f_angle_d	0.86	13535
X-RAY DIFFRACTION	f_chiral_restr	0.058	1494
X-RAY DIFFRACTION	f_plane_restr	0.005	1748
X-RAY DIFFRACTION	f_dihedral_angle_d	4.014	8166

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7769-1.7971	0.3098	80	0.2715	1699	1779	39
1.7971-1.8182	0.358	139	0.2822	2500	2639	57
1.8182-1.8404	0.2625	166	0.2611	3017	3183	68
1.8404-1.8637	0.2797	169	0.2383	3305	3474	76
1.8637-1.8882	0.2608	167	0.2283	3480	3647	80
1.8882-1.9141	0.2514	202	0.22	3650	3852	83
1.9141-1.9414	0.2522	179	0.2153	3765	3944	85
1.9414-1.9704	0.2615	241	0.2066	3901	4142	89
1.9704-2.0012	0.2557	251	0.2026	4094	4345	94
2.0012-2.034	0.2196	221	0.1971	4294	4515	97
2.034-2.0691	0.2353	213	0.1975	4341	4554	98
2.0691-2.1067	0.2107	210	0.1939	4330	4540	98
2.1067-2.1472	0.2057	236	0.1865	4287	4523	98
2.1472-2.191	0.2147	223	0.1787	4343	4566	98
2.191-2.2386	0.2169	193	0.168	4307	4500	98
2.2386-2.2907	0.1982	233	0.1637	4329	4562	98
2.2907-2.3479	0.2006	250	0.1638	4331	4581	98
2.3479-2.4114	0.1837	202	0.1665	4320	4522	97
2.4114-2.4823	0.2038	241	0.1707	4270	4511	97
2.4823-2.5624	0.1995	267	0.1657	4267	4534	97
2.5624-2.6539	0.2201	230	0.1667	4269	4499	97
2.6539-2.7601	0.1994	253	0.1625	4307	4560	96
2.7601-2.8856	0.176	211	0.1591	4265	4476	96
2.8856-3.0376	0.1709	203	0.1553	4327	4530	96
3.0376-3.2277	0.1622	199	0.1597	4283	4482	96
3.2277-3.4766	0.1937	242	0.1489	4249	4491	95
3.4766-3.8257	0.1601	230	0.1334	4248	4478	95
3.8257-4.3778	0.1514	218	0.122	4280	4498	94
4.3778-5.5097	0.1499	214	0.1222	4256	4470	93
5.5097-29.491	0.1344	235	0.1434	4291	4526	91

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	2.7681	-0.2658	0.5231	0.602	-0.906	1.3708	0.0096	0.1368	-0.0191	-0.0922	-0.0065	-0.2138	0.0632	0.2333	-0.0076	0.2969	0.0368	0.0949	0.4339	0.0498	0.3316	80.3475	-24.3579	-66.4076
2	0.9597	0.2445	0.0761	0.5316	0.1831	0.4441	0.0444	0.032	0.0292	-0.063	0.0078	-0.1204	0.0357	0.1559	-0.0167	0.2698	0.2063	0.0164	0.3758	0.0076	0.2073	82.6938	-38.0543	-52.188
3	0.2848	-0.0265	-0.1504	0.2829	0.0334	0.4127	0.018	-0.1697	-0.0405	0.0385	0.0297	-0.0118	0.2074	0.3323	0.03	0.2692	0.1066	-0.0206	0.137	0.039	0.05	62.0113	-28.1679	-38.2788
4	0.7587	-0.0116	-0.2667	0.4619	0.0015	1.1741	0.0772	0.0485	0.2231	-0.0217	0.0573	-0.2262	-0.1554	0.2305	-0.0444	0.1932	0.0477	-0.0068	0.6457	0.008	0.3823	90.4476	-22.6468	-42.1542
5	0.3998	0.6915	0.206	1.6321	0.1552	1.2214	-0.0014	-0.0523	-0.1543	0.0025	-0.0069	-0.0269	0.17	0.0407	-0.0262	0.3652	0.0418	0.0151	0.1034	0.083	0.1838	50.981	-48.6778	-41.5683
6	0.4983	0.1283	0.0024	0.5819	-0.0437	0.0578	0.0391	-0.007	-0.0914	0.0386	0.0148	0.0261	0.0947	0.0387	0.0151	0.4247	0.1376	-0.0153	0.083	0.0188	0.1809	58.1162	-50.6187	-60.0609
7	0.301	-0.0734	0.1098	0.1958	-0.0361	0.5304	0.0031	0.0787	0.0238	-0.0784	-0.0445	-0.0574	0.0723	0.2241	0.033	0.2337	0.0368	0.0065	0.0899	0.0353	0.0993	56.7632	-21.6754	-60.2977
8	0.194	-0.1637	0.078	0.6907	0.0532	0.1166	0.0149	0.074	0.0044	-0.1018	-0.0599	0.0295	0.0714	0.053	-0.0256	0.3157	0.073	-0.0243	0.0484	0.0318	0.0649	49.933	-25.4451	-70.135
9	0.7487	0.2432	0.2592	0.7382	0.1103	0.5044	0.0114	0.0284	-0.0385	-0.0466	0.0026	0.0765	0.2077	0.0749	-0.0082	0.2978	0.0667	0.021	0.1151	0.0137	0.1203	52.2099	-37.3624	-66.2316
10	1.1513	0.1022	-0.4073	0.5331	-0.2984	1.179	0.0608	-0.0598	-0.0507	0.0655	0.0398	0.1147	0.0847	-0.1199	-0.0213	0.4056	0.0005	-0.0044	0.1107	0.0347	0.2349	40.8673	-50.5924	-61.6984
11	0.78	0.9535	-0.184	1.1989	-0.0564	0.9078	-0.0762	0.0887	0.0108	-0.1482	0.0558	0.1646	0.0604	-0.1785	0.0415	0.3256	-0.1344	-0.195	0.2233	0.0781	0.3703	7.8703	-12.4062	-81.6539
12	0.0764	0.0915	0.0125	0.4157	-0.0061	0.0591	0.0234	0.0441	0.0015	-0.0396	0.0839	0.137	0.042	-0.1248	0.0023	0.2191	-0.163	-0.0846	0.3179	0.2315	0.5219	-1.6312	-14.1366	-64.124
13	0.0789	0.0523	-0.0338	0.1807	-0.1057	0.1818	0.0583	-0.0507	-0.006	0.0722	0.1047	0.2863	-0.0406	-0.1744	0.0296	0.1763	0.0061	0.0604	-0.1001	0.1278	0.227	23.199	-3.6274	-53.259
14	0.4024	0.4067	0.0928	0.7059	0.1037	0.2021	0.0157	-0.0299	-0.084	-0.0097	0.0318	0.0722	0.0859	-0.0524	-0.0179	0.2108	-0.0221	0.0439	0.0263	0.0626	0.1996	27.0864	-15.0935	-47.1632
15	0.077	0.0646	0.1172	0.3258	-0.1151	0.3713	0.0554	-0.0495	0.0307	0.0747	0.1086	0.2171	0.0117	-0.2237	-0.0753	0.155	0.0046	0.0796	0.1551	0.1338	0.3839	11.5792	-6.1921	-49.2909
16	0.2033	0.2822	-0.0409	0.7194	0.0823	0.3602	0.052	0.0442	-0.0738	-0.1055	0.1054	0.0162	0.1415	-0.0847	0.0603	0.4205	-0.2512	-0.1539	0.1659	0.1427	0.5207	9.0354	-30.5103	-63.1201

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 36 through 61 )	A	36 - 61
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 62 through 105 )	A	62 - 105
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 106 through 344 )	A	106 - 344
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 345 through 439 )	A	345 - 439
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 36 through 61 )	B	36 - 61
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 62 through 105 )	B	62 - 105
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 106 through 220 )	B	106 - 220
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 221 through 295 )	B	221 - 295
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 296 through 389 )	B	296 - 389
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 390 through 439 )	B	390 - 439
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 36 through 61 )	C	36 - 61
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 62 through 105 )	C	62 - 105
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 106 through 220 )	C	106 - 220
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 221 through 263 )	C	221 - 263
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 264 through 344 )	C	264 - 344
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 345 through 439 )	C	345 - 439

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