PDB-9izl: hVanin-1 complexed with X17

ID or keywords:

Entry

Database: PDB / ID: 9izl

Title

hVanin-1 complexed with X17

Components

Pantetheinase

Keywords

MEMBRANE PROTEIN / Inhibitor / complex / hVanin-1 / HYDROLASE

Function / homology

Function and homology information

pantetheine hydrolase / pantetheine hydrolase activity / pantothenate metabolic process / chronic inflammatory response / coenzyme A catabolic process / Vitamin B5 (pantothenate) metabolism / positive regulation of T cell differentiation in thymus / Post-translational modification: synthesis of GPI-anchored proteins / acute inflammatory response / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.28 Å

Authors

Fan, S. / Zhen, L. / Xie, T.

Funding support

China, 1items

Citation

Journal: J.Med.Chem. / Year: 2024
Title: Discovery of Thiazole Carboxamides as Novel Vanin-1 Inhibitors for Inflammatory Bowel Disease Treatment.
Authors: Xie, T. / Cao, G.Y. / Zhang, S. / Li, M.K. / Jin, X. / Liu, L. / Wang, G. / Zhen, L.

History

Deposition	Aug 1, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Dec 4, 2024	Provider: repository / Type: Initial release
Revision 1.1	Dec 11, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9izl.cif.gz	378.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9izl.ent.gz		Display	PDB format
PDBx/mmJSON format	9izl.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/iz/9izl ftp://data.pdbj.org/pub/pdb/validation_reports/iz/9izl	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

Deposited unit

A: Pantetheinase

B: Pantetheinase

hetero molecules

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

1

A: Pantetheinase

hetero molecules

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

2

B: Pantetheinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.823, 92.980, 218.923
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Pantetheinase / Pantetheine hydrolase / Tiff66 / Vascular non-inflammatory molecule 1 / Vanin-1 Mass: 51585.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VNN1 / Production host: Homo sapiens (human) / References: UniProt: O95497, pantetheine hydrolase
#2: Chemical	ChemComp-A1EAG / 8-oxa-2-azaspiro[4.5]decan-2-yl-[2-[(3~{S})-3-oxidanylpyrrolidin-1-yl]-1,3-thiazol-5-yl]methanone Mass: 337.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₂₃N₃O₃S / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.89 Å³/Da / Density % sol: 57.43 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M TMAO, 0.1 M Tris 8.5, 20% w/v PEG 2000 MME.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL02U1 / Wavelength: 0.9789 Å

Detector

Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 20, 2024

Radiation

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

Radiation wavelength

Wavelength: 0.9789 Å / Relative weight: 1

Reflection

Resolution: 2.28→50 Å / Num. obs: 53547 / % possible obs: 95.6 % / Redundancy: 10.9 % / CC_1/2: 0.998 / CC star: 0.999 / R_merge(I) obs: 0.166 / R_pim(I) all: 0.051 / R_rim(I) all: 0.174 / Χ²: 0.787 / Net I/σ(I): 3.7 / Num. measured all: 583939

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.28-2.32	6.5	0.873	1820	0.874	0.966	0.307	0.93	0.458	67.1
2.32-2.36	6.8	0.907	2079	0.879	0.967	0.315	0.965	0.452	74.8
2.36-2.41	7.2	0.996	2312	0.851	0.959	0.345	1.06	0.459	84.1
2.41-2.46	7.5	0.965	2624	0.84	0.955	0.337	1.029	0.464	94.4
2.46-2.51	8.9	1.083	2722	0.886	0.969	0.363	1.146	0.456	99.1
2.51-2.57	10.9	1.167	2783	0.914	0.977	0.36	1.223	0.44	100
2.57-2.63	12.3	1.02	2736	0.95	0.987	0.299	1.064	0.471	100
2.63-2.7	12.7	0.914	2781	0.947	0.986	0.263	0.952	0.476	100
2.7-2.78	12.8	0.779	2753	0.96	0.99	0.224	0.811	0.482	100
2.78-2.87	12.2	0.598	2767	0.971	0.993	0.176	0.623	0.534	100
2.87-2.98	11.8	0.47	2799	0.974	0.994	0.142	0.491	0.572	100
2.98-3.09	13.3	0.408	2798	0.987	0.997	0.115	0.424	0.606	99.9
3.09-3.24	13.2	0.308	2776	0.991	0.998	0.088	0.321	0.674	100
3.24-3.41	12.8	0.227	2786	0.993	0.998	0.066	0.237	0.811	99.8
3.41-3.62	12.5	0.177	2782	0.995	0.999	0.052	0.185	0.967	99.5
3.62-3.9	11.7	0.13	2816	0.996	0.999	0.04	0.136	1.159	99.3
3.9-4.29	10.6	0.097	2779	0.997	0.999	0.031	0.103	1.272	98.3
4.29-4.91	9.9	0.073	2770	0.997	0.999	0.025	0.078	1.438	96.7
4.91-6.19	10.5	0.07	2841	0.997	0.999	0.023	0.074	1.377	98.9
6.19-50	10.5	0.053	3023	0.998	0.999	0.018	0.056	1.671	98.7

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.28→31.87 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.59 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2597	1995	3.82 %
R_work	0.215	-	-
obs	0.2167	52274	93.26 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.28→31.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7262	0	46	130	7438

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_dihedral_angle_d	11.304	1018
X-RAY DIFFRACTION	f_chiral_restr	0.061	1124
X-RAY DIFFRACTION	f_plane_restr	0.013	1330

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 (%)
2.28-2.33	0.3656	93	0.3346	2362	X-RAY DIFFRACTION	62
2.33-2.4	0.4012	115	0.3204	2888	X-RAY DIFFRACTION	76
2.4-2.47	0.3819	136	0.3113	3404	X-RAY DIFFRACTION	90
2.47-2.55	0.3401	145	0.2892	3657	X-RAY DIFFRACTION	96
2.55-2.64	0.3373	147	0.273	3678	X-RAY DIFFRACTION	96
2.64-2.74	0.3278	146	0.257	3708	X-RAY DIFFRACTION	97
2.74-2.87	0.3269	146	0.2509	3691	X-RAY DIFFRACTION	98
2.87-3.02	0.3246	149	0.2393	3781	X-RAY DIFFRACTION	98
3.02-3.21	0.3015	149	0.239	3773	X-RAY DIFFRACTION	99
3.21-3.45	0.2848	153	0.2126	3845	X-RAY DIFFRACTION	99
3.45-3.8	0.2462	151	0.2078	3793	X-RAY DIFFRACTION	99
3.8-4.35	0.2191	152	0.1825	3809	X-RAY DIFFRACTION	98
4.35-5.48	0.2033	152	0.164	3818	X-RAY DIFFRACTION	97

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	2.7893	0.2339	0.3632	2.8289	1.0767	3.5686	0.1599	0.0696	0.3305	-0.6571	-0.0567	0.526	-0.1231	-0.3274	-0.0918	0.4034	0.0323	-0.0122	0.5337	0.0613	0.3606	-17.7271	12.9431	14.0561
2	1.5185	0.8068	0.7759	3.2645	0.9027	2.6574	0.1033	-0.1149	0.1001	-0.0934	-0.0156	0.0938	0.0133	-0.0582	-0.056	0.2756	0.0272	0.0011	0.4053	0.0459	0.3176	-8.7038	15.306	18.7066
3	2.6879	-0.2382	0.5028	3.6326	-0.6716	4.068	0.2013	0.231	0.1418	-0.051	0.0373	-0.312	-0.1592	0.4696	-0.1244	0.3758	-0.0078	0.013	0.4419	0.0025	0.3781	0.5511	13.5071	11.8518
4	1.5675	0.6762	-0.0277	1.618	0.8706	3.5375	-0.0515	-0.0883	-0.1174	-0.1102	0.1931	-0.2817	0.4384	0.0007	-0.1556	0.6292	0.0907	-0.0333	0.4193	0.0213	0.4482	-3.2621	-0.7456	3.5867
5	1.9174	-0.2304	-1.521	1.0791	0.9003	4.2849	-0.046	-0.0433	-0.192	0.1205	0.0471	-0.0371	0.6381	-0.0043	-0.0029	0.682	-0.0698	-0.1149	0.4288	-0.009	0.4303	-11.3547	-5.4879	3.5879
6	2.4706	0.9335	-0.3322	2.6502	1.403	4.3277	-0.0514	0.4787	-0.1884	-0.8228	0.2083	-0.1086	0.287	0.5482	-0.1212	1.0917	0.1645	-0.0399	0.6438	-0.0365	0.4509	-4.2671	-9.0131	-18.4027
7	3.6643	0.9872	-0.7032	1.5721	-0.6819	7.2111	-0.003	0.1324	0.2782	-0.6667	-0.178	0.1995	-0.3642	-0.1519	0.2504	0.7165	0.0515	-0.0692	0.4563	0.0228	0.5149	-16.564	-5.1428	-18.8549
8	4.2688	0.6894	0.7582	2.0153	1.2107	4.3032	0.3724	0.0281	-0.7922	-0.315	-0.0519	-0.1693	1.0236	0.3318	-0.2406	0.9411	0.1503	-0.0931	0.4348	-0.0135	0.4843	-5.7287	-12.3177	-6.2482
9	1.8696	-0.3648	-1.7486	2.3727	-0.2059	1.8011	0.3495	0.5179	-0.6738	0.0392	-0.0778	0.2532	0.8874	-0.139	-0.2478	0.6884	-0.0569	-0.0538	0.3924	-0.0274	0.319	-26.4244	2.6264	-44.1735
10	1.4316	-1.142	0.1158	3.1653	1.2509	3.861	-0.1026	0.0075	-0.1069	0.3481	0.0608	0.1797	0.4508	-0.349	0.0221	0.4863	-0.1085	0.013	0.4027	0.0042	0.3533	-31.1292	9.8046	-37.471
11	3.0131	-0.8526	-0.8251	2.8806	0.2117	2.5511	-0.0547	0.1498	-0.1042	0.2193	0.2551	-0.0119	0.1066	0.0724	-0.0913	0.3997	-0.0024	-0.0472	0.3298	-0.0771	0.3417	-23.5182	16.9316	-42.1613
12	1.8121	-1.0677	-1.1462	2.8293	-0.8765	3.6407	-0.1241	-0.0308	-0.0801	0.1494	0.2763	-0.3423	0.4875	0.3622	-0.1478	0.4362	-0.0084	-0.0982	0.4327	-0.0731	0.3832	-13.2593	7.2322	-49.999
13	3.7484	1.4101	1.0874	1.9771	0.9584	2.5586	-0.0901	-0.1199	-0.0227	-0.209	0.2558	-0.4291	-0.4179	0.3575	-0.0908	0.617	-0.129	-0.001	0.6286	-0.0487	0.603	0.7899	15.6891	-68.0553
14	2.9869	-0.7724	-0.692	4.6141	1.1738	2.6547	-0.054	0.3357	0.3311	-0.4828	-0.0708	-0.3254	-0.587	0.5159	0.0998	0.5577	-0.1587	0.0149	0.7376	-0.0591	0.5315	-1.4133	11.723	-74.9586
15	3.2616	-1.3631	-0.6953	4.7648	0.7285	3.0546	0.1044	0.0106	-0.0427	-0.1984	0.1917	-0.2895	-0.0599	0.3987	-0.2371	0.3701	-0.0601	-0.0299	0.5358	-0.07	0.3665	-5.4144	9.529	-69.6968
16	3.899	-0.9775	0.883	4.1936	-0.1997	3.9041	0.2448	-0.0873	0.0067	0.0445	0.0826	-0.2628	0.3568	0.1873	-0.2319	0.5844	-0.1037	-0.0008	0.6293	-0.1094	0.4536	-9.5568	-0.4589	-73.519
17	3.3488	0.444	-1.0548	1.4391	-0.2213	1.9587	0.1453	-0.4284	0.3521	0.216	-0.1561	-0.5634	0.184	0.637	-0.0523	0.4596	-0.0018	-0.088	0.6067	-0.1095	0.5222	-0.2544	7.9012	-59.5634
18	2.6951	-0.7602	-1.4113	3.9205	1.3511	2.0036	-0.1265	0.0182	0.4528	0.5855	0.3727	-1.0267	-0.0144	0.6264	-0.311	0.4415	-0.0257	-0.1276	0.6059	-0.1105	0.5221	-3.5723	9.844	-61.1288

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 48 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 123 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 124 through 189 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 190 through 245 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 246 through 301 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 302 through 381 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 382 through 400 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 401 through 462 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 24 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 25 through 135 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 136 through 189 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 190 through 288 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 289 through 318 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 319 through 339 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 340 through 381 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 382 through 400 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 401 through 438 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 439 through 462 )

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