PDB-5w4b: The crystal structure of human S-adenosylhomocysteine hydrolase (...

ID or keywords:

Entry

Database: PDB / ID: 5w4b

Title

The crystal structure of human S-adenosylhomocysteine hydrolase (AHCY) bound to benzothiazole inhibitor

Components

Adenosylhomocysteinase

Keywords

HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

Function and homology information

Defective AHCY causes HMAHCHD / Sulfur amino acid metabolism / Metabolism of ingested SeMet, Sec, MeSec into H2Se /

adenosylhomocysteinase / S-adenosylmethionine cycle /

adenosylhomocysteinase activity /

Methylation /

melanosome / one-carbon metabolic process /

endoplasmic reticulum ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Dougan, D.R. / Lawson, J.D. / Lane, W.

Citation

Journal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Identification of AHCY inhibitors using novel high-throughput mass spectrometry.
Authors: Uchiyama, N. / Dougan, D.R. / Lawson, J.D. / Kimura, H. / Matsumoto, S.I. / Tanaka, Y. / Kawamoto, T.

History

Deposition	Jun 9, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 28, 2017	Provider: repository / Type: Initial release
Revision 1.1	Aug 16, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5w4b.cif.gz	1001.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5w4b.ent.gz	844 KB	Display	PDB format
PDBx/mmJSON format	5w4b.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/w4/5w4b ftp://data.pdbj.org/pub/pdb/validation_reports/w4/5w4b	HTTPS FTP

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Related structure data

Related structure data	5w49C C: citing same article (ref.)
Similar structure data	1b3r-d 4yvf-1 1xwf-d 1ky4-d 5w49-1 6e5y-2 3gvp-d 3g1u-d 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: Adenosylhomocysteinase

B: Adenosylhomocysteinase

C: Adenosylhomocysteinase

D: Adenosylhomocysteinase

E: Adenosylhomocysteinase

F: Adenosylhomocysteinase

hetero molecules

291 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Adenosylhomocysteinase

B: Adenosylhomocysteinase

E: Adenosylhomocysteinase

F: Adenosylhomocysteinase

hetero molecules

defined by author&software
194 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Adenosylhomocysteinase

D: Adenosylhomocysteinase

hetero molecules

C: Adenosylhomocysteinase

D: Adenosylhomocysteinase

hetero molecules

defined by author&software
194 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.511, 406.464, 186.724
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	D-785- HOH

#1: Protein	Adenosylhomocysteinase / / AdoHcyase / S-adenosyl-L-homocysteine hydrolase Mass: 47439.598 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AHCY, SAHH / Plasmid: pSX70 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2(DE3) pLysS / References: UniProt: P23526, adenosylhomocysteinase
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-9W4 / 4-[(2,5-dioxo-2,5-dihydro-1H-imidazol-1-yl)methyl]-N-[2-(morpholin-4-yl)-1,3-benzothiazol-6-yl]benzamide Mass: 449.482 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₂H₁₉N₅O₄S
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1249 / 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: 3.15 Å³/Da / Density % sol: 60.95 % / Mosaicity: 0.5 °
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 8-12% PEG8000, 0.12 M ethylene glycol, 0.1 M Tris(base):Bicine, pH 8.5

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.3 / Wavelength: 0.9765 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2015

Radiation

Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9765 Å / Relative weight: 1

Reflection

Resolution: 2.65→50 Å / Num. obs: 104368 / % possible obs: 99.4 % / Redundancy: 7.2 % / R_merge(I) obs: 0.237 / R_pim(I) all: 0.094 / R_rim(I) all: 0.256 / Χ²: 1.003 / Net I/σ(I): 3.6 / Num. measured all: 754661

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.65-2.7	7.1	0.959	0.83	0.385	1.034	0.942	98.9
2.7-2.74	7.2	0.923	0.824	0.366	0.993	0.974	99
2.74-2.8	7.3	0.794	0.871	0.314	0.854	0.992	99
2.8-2.85	7.3	0.743	0.892	0.292	0.799	0.982	99.1
2.85-2.92	7.4	0.7	0.912	0.275	0.753	1	99.1
2.92-2.98	7.3	0.598	0.915	0.236	0.643	1.018	99.2
2.98-3.06	7.3	0.541	0.935	0.213	0.582	1.032	99.2
3.06-3.14	7.3	0.457	0.95	0.18	0.491	1.025	99.3
3.14-3.23	7.3	0.405	0.969	0.16	0.436	1.032	99.3
3.23-3.34	7.3	0.315	0.974	0.124	0.339	1.02	99.3
3.34-3.46	7.3	0.245	0.986	0.097	0.264	1.007	99.4
3.46-3.6	7.3	0.206	0.99	0.081	0.221	1.009	99.4
3.6-3.76	7.3	0.185	0.991	0.073	0.199	1	99.5
3.76-3.96	7.2	0.159	0.994	0.063	0.171	0.987	99.5
3.96-4.21	7.2	0.144	0.994	0.057	0.155	1.003	99.6
4.21-4.53	7.2	0.118	0.997	0.047	0.127	1.01	99.6
4.53-4.99	7.1	0.106	0.998	0.042	0.114	0.984	99.7
4.99-5.71	6.9	0.135	0.996	0.055	0.146	1.031	99.8
5.71-7.19	7.1	0.135	0.997	0.054	0.145	1.023	99.7
7.19-50	7	0.055	1	0.022	0.059	0.987	99.8

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
HKL-2000		data scaling
REFMAC	5.8.0135	refinement
PDB_EXTRACT	3.22	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.65→30 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.915 / SU B: 20.328 / SU ML: 0.235 / SU R Cruickshank DPI: 0.7171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.717 / ESU R Free: 0.304 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2405	5287	5.1 %	RANDOM
R_work	0.1994	-	-	-
obs	0.2015	99028	99.17 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 135.46 Å² / B_iso mean: 42.891 Å² / B_iso min: 2.8 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.15 Å²	0 Å²	0 Å²
2-	-	-1.93 Å²	-0 Å²
3-	-	-	2.09 Å²

Refinement step

Cycle: final / Resolution: 2.65→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19896	0	537	1249	21682
B_iso mean	-	-	36.36	27.26	-
Num. residues	-	-	-	-	2570

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	20898
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	19850
X-RAY DIFFRACTION	r_angle_refined_deg	1.269	1.992	28362
X-RAY DIFFRACTION	r_angle_other_deg	1.255	3	45697
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.857	5	2570
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.43	24.708	873
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.634	15	3578
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.442	15	102
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	3149
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	23522
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4533

LS refinement shell

Resolution: 2.645→2.714 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.32	376	-
R_work	0.293	7070	-
all	-	7446	-
obs	-	-	96.95 %

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	0.3523	0.4132	0.0852	0.9497	-0.2484	0.4845	0.0259	-0.1634	0.4377	0.0376	-0.2467	0.3019	0.1419	0.1121	0.2208	0.1034	0.0648	-0.0076	0.1412	-0.2016	0.6503	16.706	95.6639	213.6214
2	0.3277	0.1966	-0.1003	0.4529	0.015	0.0628	-0.0188	-0.0087	0.112	0.0941	0.0201	-0.0424	0.0436	-0.0307	-0.0013	0.1945	0.0024	0.0001	0.2119	-0.0325	0.2904	30.34	79.5945	200.8928
3	0.1505	-0.0282	-0.0684	0.9787	0.1368	0.1042	-0.0201	0.0864	-0.0602	0.1987	0.0208	0.002	0.0524	0.016	-0.0008	0.3136	0.0163	0.048	0.1973	0.0658	0.1915	34.6451	37.5489	211.6912
4	0.0712	-0.1218	0.1591	0.5098	-0.181	0.4177	-0.0315	0.0084	-0.008	0.0349	0.0138	0.1233	-0.0245	0.0974	0.0177	0.2041	-0.0087	0.0763	0.2053	-0.026	0.2725	15.8568	56.6111	196.2571
5	1.6238	1.0741	0.0142	1.0899	0.3535	0.4484	0.0793	-0.0148	-0.1158	0.136	-0.0135	0.0425	0.1402	0.0407	-0.0657	0.2237	-0.0136	0.0228	0.1254	0.0025	0.3211	9.1482	42.7008	191.7223
6	0.0287	-0.0561	-0.0545	1.8164	-0.2655	0.1937	-0.0437	0.0307	-0.0284	0.2764	-0.0481	-0.1138	-0.0144	-0.033	0.0918	0.2795	0.0077	-0.0847	0.2413	-0.0389	0.2043	39.6236	61.0165	211.6623
7	0.2732	-0.0013	-0.2815	0.7601	-0.1704	0.5043	-0.0634	0.0386	0.138	-0.0307	-0.0241	-0.1733	0.048	-0.0656	0.0875	0.1785	0.0262	0.0302	0.1571	0.0858	0.4001	-7.9001	28.4782	163.3721
8	0.7474	0.1307	0.423	0.1962	0.0408	0.284	-0.1131	0.0076	0.1552	-0.1541	-0.0199	0.0475	0.0486	0.0112	0.133	0.3452	0.0237	0.0545	0.1915	0.15	0.1984	-18.6614	25.3979	149.2259
9	0.1609	0.1234	-0.1469	0.2769	-0.3679	0.7502	-0.0047	-0.0191	0.0513	-0.0456	-0.081	-0.0378	0.0649	0.0859	0.0857	0.2291	0.0088	-0.0006	0.1919	0.0148	0.2471	-26.4259	9.2084	173.1794
10	0.955	-0.6719	0.0546	1.2988	0.3644	0.2038	-0.024	0.0372	0.0406	-0.041	-0.0088	0.1204	-0.0253	0.0121	0.0328	0.1989	0.016	-0.0087	0.1658	0.0089	0.2932	-39.3216	19.3349	178.3119
11	0.0195	-0.1096	0.0609	1.6469	-0.6811	0.3026	-0.0208	-0.0313	0.0307	-0.2744	-0.0588	-0.1984	0.0708	-0.0302	0.0796	0.2721	0.0478	0.1378	0.2196	0.0104	0.2341	-7.4091	4.1392	160.3108
12	0.0689	-0.1671	-0.0027	0.7646	-0.1265	0.1325	-0.0496	0.0531	0.0192	0.1676	0.0612	-0.0332	-0.0627	-0.0368	-0.0116	0.3187	0.0122	-0.0153	0.1905	-0.0565	0.2117	-30.0751	30.6789	211.813
13	0.1135	-0.1782	-0.0665	0.3238	0.0478	0.3416	0.0164	0.0158	0.0398	0.0527	-0.0154	-0.1388	-0.0168	-0.1066	-0.001	0.2376	-0.0285	-0.0358	0.2115	0.0267	0.2712	-15.2985	10.164	198.5851
14	1.1268	0.5186	-0.2425	0.9301	-0.5033	0.4168	0.0946	-0.0449	-0.0303	0.0231	-0.0767	-0.1204	-0.1172	-0.0301	-0.0179	0.1989	-0.0242	-0.0077	0.133	0.0134	0.3315	-2.9209	21.2318	192.5345
15	0.027	-0.0396	0.0584	1.7502	0.2719	0.2281	-0.0486	0.015	0.0158	0.2603	-0.0105	0.0274	-0.0179	-0.0344	0.059	0.296	-0.014	0.0956	0.236	-0.0205	0.1903	-34.9818	7.2138	212.2385
16	0.065	0.0988	-0.1223	0.7592	-0.0516	0.3456	-0.0673	-0.0348	-0.0285	-0.111	0.0324	0.0955	0.0695	0.0693	0.0349	0.2552	-0.0088	-0.0139	0.2181	-0.0922	0.2288	17.0521	39.8529	157.4547
17	0.1344	0.1763	0.1976	0.2441	0.252	0.6168	-0.0414	0.0076	-0.0308	-0.0452	-0.0387	-0.0548	-0.0155	-0.0845	0.08	0.2217	0.0116	0.0215	0.2262	0.0047	0.2383	32.1536	58.7034	172.8699
18	1.2155	-0.785	0.0358	1.1482	-0.2582	0.0918	0.0237	0.0478	-0.0892	-0.0658	-0.0451	-0.0709	0.0395	0.0138	0.0214	0.1958	0.0085	0.0178	0.2096	-0.0119	0.2497	44.4344	47.0664	177.9882
19	0.0098	-0.1222	-0.0583	1.681	0.7793	0.3644	0.0094	0.0023	-0.0158	-0.2203	-0.0762	0.1299	-0.0785	-0.0327	0.0668	0.2749	0.0388	-0.1017	0.2527	0.0072	0.2024	12.5899	63.0585	159.3131
20	0.3783	-0.2361	0.1874	0.6053	0.3025	0.7172	0.0007	0.0883	0.2804	-0.0707	-0.0971	-0.0708	0.0903	0.0172	0.0963	0.2048	-0.0244	-0.0431	0.1587	0.1559	0.3631	35.4427	96.6856	159.2057
21	0.3588	-0.4199	-0.0857	0.6795	0.0046	0.1434	-0.003	0.021	0.0653	-0.0051	-0.0108	0.0749	0.084	0.0813	0.0138	0.1872	0.0126	0.0039	0.2095	0.0229	0.2987	16.5498	77.1333	177.4345
22	0.725	-0.6863	-0.0759	0.9905	0.3491	0.2584	0.0033	0.0358	0.0666	-0.0684	-0.0449	0.0823	-0.0708	0.023	0.0416	0.147	0.0329	0.0063	0.162	0.0155	0.3719	8.4428	91.2405	179.7103
23	0.02	-0.1577	0.0919	1.7731	-0.6952	0.43	-0.0074	0.0062	0.0136	-0.242	-0.0241	-0.1105	-0.0037	0.0401	0.0315	0.2538	-0.0022	0.1036	0.2588	0.0607	0.1983	40.5019	74.2355	160.1041

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 169
2	X-RAY DIFFRACTION	2	A	170 - 432
3	X-RAY DIFFRACTION	3	B	4 - 169
4	X-RAY DIFFRACTION	4	B	170 - 298
5	X-RAY DIFFRACTION	5	B	299 - 354
6	X-RAY DIFFRACTION	6	B	355 - 432
7	X-RAY DIFFRACTION	7	C	5 - 106
8	X-RAY DIFFRACTION	8	C	107 - 169
9	X-RAY DIFFRACTION	9	C	170 - 255
10	X-RAY DIFFRACTION	10	C	256 - 354
11	X-RAY DIFFRACTION	11	C	355 - 432
12	X-RAY DIFFRACTION	12	D	4 - 169
13	X-RAY DIFFRACTION	13	D	170 - 261
14	X-RAY DIFFRACTION	14	D	262 - 354
15	X-RAY DIFFRACTION	15	D	355 - 432
16	X-RAY DIFFRACTION	16	E	5 - 169
17	X-RAY DIFFRACTION	17	E	170 - 261
18	X-RAY DIFFRACTION	18	E	262 - 354
19	X-RAY DIFFRACTION	19	E	355 - 432
20	X-RAY DIFFRACTION	20	F	5 - 183
21	X-RAY DIFFRACTION	21	F	184 - 283
22	X-RAY DIFFRACTION	22	F	284 - 354
23	X-RAY DIFFRACTION	23	F	355 - 432

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+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