PDB-5brn: Human HGPRT in complex with (S)-HPEPHx, an acyclic nucleoside pho...

ID or keywords:

Entry

Database: PDB / ID: 5brn

Title

Human HGPRT in complex with (S)-HPEPHx, an acyclic nucleoside phosphonate

Components

Hypoxanthine-guanine phosphoribosyltransferase

Keywords

TRANSFERASE/TRANSFERASE Inhibitor / Hypoxanthine-guanine-xanthine phosphoribosyltransferase / acyclic nuclesoside phosphonates / inhibitor / TRANSFERASE-TRANSFERASE Inhibitor complex

Function / homology

Function and homology information

adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine salvage / hypoxanthine metabolic process / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / hypoxanthine phosphoribosyltransferase / lymphocyte proliferation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Keough, D.T. / Guddat, L.W. / Kaiser, M.M. / Hockova, D. / Wang, T.-H. / Janeba, Z.

Citation

Journal: Chemmedchem / Year: 2015
Title: Synthesis and Evaluation of Novel Acyclic Nucleoside Phosphonates as Inhibitors of Plasmodium falciparum and Human 6-Oxopurine Phosphoribosyltransferases.
Authors: Kaiser, M.M. / Hockova, D. / Wang, T.H. / Dracinsky, M. / Postova-Slavetinska, L. / Prochazkova, E. / Edstein, M.D. / Chavchich, M. / Keough, D.T. / Guddat, L.W. / Janeba, Z.

History

Deposition	May 31, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5brn.cif.gz	328.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5brn.ent.gz	267.6 KB	Display	PDB format
PDBx/mmJSON format	5brn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5brn_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	5brn_full_validation.pdf.gz	1.6 MB	Display
Data in XML	5brn_validation.xml.gz	33.2 KB	Display
Data in CIF	5brn_validation.cif.gz	44.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/br/5brn ftp://data.pdbj.org/pub/pdb/validation_reports/br/5brn	HTTPS FTP

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Related structure data

Related structure data	5bskC 4ijqS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6bnj-d 6i98-d 5fp1-d 5bsk-d 5n0v-d 6tsc-1 5ipf-d 4ran-d 3qlb-2 1xkw-d 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
Related items in Molecule of the Month	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (8)

Deposited unit

A: Hypoxanthine-guanine phosphoribosyltransferase

B: Hypoxanthine-guanine phosphoribosyltransferase

C: Hypoxanthine-guanine phosphoribosyltransferase

D: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	64.530, 94.310, 139.270
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Hypoxanthine-guanine phosphoribosyltransferase / HGPRTase Mass: 24516.217 Da / Num. of mol.: 4 / Mutation: C22A, C105A, C205A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HPRT1, HPRT / Production host: Escherichia coli (E. coli) References: UniProt: P00492, hypoxanthine phosphoribosyltransferase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-4X2 / (2-{[(2S)-1-hydroxy-3-(6-oxo-1,6-dihydro-9H-purin-9-yl)propan-2-yl]oxy}ethyl)phosphonic acid Mass: 318.223 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₄O₆P
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.15 Å³/Da / Density % sol: 42.85 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 20% PEG3000, 0.2 M calcium acetate, 0.1 M Tris-HCl pH 7.4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 12, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95369 Å / Relative weight: 1
Reflection	Resolution: 2.3→53.3 Å / Num. obs: 37163 / % possible obs: 90.4 % / Redundancy: 4.1 % / R_merge(I) obs: 0.065 / Net I/σ(I): 12.9

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
SCALA		data scaling
PHASER		phasing
MOSFLM		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4IJQ

4ijq

Resolution: 2.3→47.332 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2919	2000	5.39 %
R_work	0.239	-	-
obs	0.2418	37136	96.39 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→47.332 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6127	0	88	266	6481

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6339
X-RAY DIFFRACTION	f_angle_d	0.708	8604
X-RAY DIFFRACTION	f_dihedral_angle_d	12.695	2333
X-RAY DIFFRACTION	f_chiral_restr	0.024	979
X-RAY DIFFRACTION	f_plane_restr	0.004	1090

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 (%)
2.3-2.3575	0.3531	131	0.301	2307	X-RAY DIFFRACTION	91
2.3575-2.4213	0.3683	132	0.3026	2302	X-RAY DIFFRACTION	90
2.4213-2.4925	0.3456	134	0.2846	2350	X-RAY DIFFRACTION	90
2.4925-2.5729	0.3582	132	0.2742	2344	X-RAY DIFFRACTION	92
2.5729-2.6649	0.3177	137	0.2727	2404	X-RAY DIFFRACTION	94
2.6649-2.7716	0.3354	142	0.2631	2482	X-RAY DIFFRACTION	97
2.7716-2.8977	0.3433	144	0.274	2532	X-RAY DIFFRACTION	98
2.8977-3.0505	0.3235	145	0.2511	2557	X-RAY DIFFRACTION	99
3.0505-3.2415	0.3251	148	0.2524	2595	X-RAY DIFFRACTION	99
3.2415-3.4917	0.3023	147	0.2348	2587	X-RAY DIFFRACTION	100
3.4917-3.843	0.2451	148	0.2106	2611	X-RAY DIFFRACTION	100
3.843-4.3987	0.2338	151	0.1989	2634	X-RAY DIFFRACTION	100
4.3987-5.5406	0.2435	150	0.2017	2651	X-RAY DIFFRACTION	100
5.5406-47.3416	0.3055	159	0.2582	2780	X-RAY DIFFRACTION	100

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	2.2031	-1.0335	-1.0846	7.6601	-1.4803	3.1589	0.3184	-0.6166	0.382	0.825	-0.5298	-0.9126	-0.3082	-0.0349	-0.2477	0.2746	-0.087	-0.0286	0.3214	-0.127	0.22	-16.8371	19.5181	-1.9416
2	0.4065	0.7642	-0.4304	1.5581	-0.2139	3.0653	0.0692	-0.1917	-0.0633	0.2147	0.1341	-0.7437	0.2724	0.6876	0.0447	0.2999	0.0015	-0.0356	0.4284	0.0078	0.3057	-11.2825	4.451	-3.7418
3	3.9015	0.4065	0.946	2.4645	-0.8233	4.4229	0.1322	-0.6241	0.5287	-0.1526	-0.024	0.2078	-0.0535	-0.8787	-0.0996	0.2471	0.0454	-0.0233	0.3225	0.0035	0.2188	-33.7456	15.2023	-7.0256
4	0.5421	1.1272	0.2239	3.0546	0.3947	2.9908	-0.0461	0.2758	0.099	0.0134	0.0319	0.35	0.0632	-0.5427	-0.0542	0.2174	0.0144	-0.0526	0.4032	0.0372	0.29	-34.5808	9.5008	-15.9093
5	2.2029	0.4745	0.1396	1.823	0.1259	3.3237	0.0134	0.1567	-0.2022	-0.047	0.033	0.121	-0.2845	-0.6802	-0.0799	0.3172	0.0876	-0.0403	0.4348	0.0091	0.2872	-35.2177	13.0674	-20.9148
6	5.9156	-0.1814	0.9736	3.8056	0.371	0.9476	-0.8788	2.1614	0.2549	-0.841	0.4177	0.5774	-1.4403	1.1595	-0.093	0.5689	-0.0107	-0.0397	0.6016	0.0128	0.3237	-28.6903	21.1084	-29.1874
7	1.4041	0.3964	-0.5084	1.5563	-0.2311	2.9839	0.1229	0.4357	0.4395	-0.2905	-0.0465	0.0724	-0.7184	-0.0428	-0.0147	0.4205	-0.018	0.0038	0.3182	0.0738	0.2905	-26.552	22.9795	-17.7933
8	1.275	0.4872	0.6601	2.5659	0.6173	1.9244	0.0801	0.198	-0.2353	-0.1501	-0.1363	-0.8778	0.1791	0.7601	-0.0155	0.1515	0.0764	0.0798	0.4336	0.036	0.3378	-12.6385	8.9176	-12.9986
9	1.329	0.4064	0.0475	2.6848	0.7425	3.2132	-0.2921	0.2051	-0.1482	0.4056	-0.0686	0.0275	0.7732	-0.7194	0.0431	0.5788	-0.1482	0.0563	0.3999	-0.0519	0.3446	-39.1154	-19.7045	-0.3345
10	0.7262	1.2941	0.5458	2.1721	0.8112	2.9226	-0.0524	0.0332	0.0222	-0.0698	0.0291	0.2576	0.0441	-0.7008	-0.0359	0.2858	-0.0179	0.0081	0.5214	0.0251	0.2868	-46.9879	0.5087	7.0565
11	1.7551	-0.1459	-0.3676	1.7579	-1.1909	3.9526	0.0999	0.0575	0.1147	-0.0151	-0.0141	-0.1586	-0.1823	0.2008	-0.0053	0.3456	-0.0508	0.0016	0.3548	-0.0511	0.333	-41.1779	3.3975	6.4129
12	1.2239	1.0901	-0.4934	2.0651	-0.2754	2.5676	0.0283	-0.1908	0.025	0.5434	0.1135	0.3606	-0.1602	-0.6427	-0.0581	0.4202	-0.0277	0.1404	0.5964	-0.0151	0.4053	-50.0746	-0.7173	17.8439
13	1.511	-0.8858	-0.6448	2.8138	-0.2356	2.5515	-0.1447	-0.177	-0.4876	0.2862	-0.0377	0.3664	0.7826	-0.4155	0.0623	0.583	-0.255	0.056	0.5071	0.0206	0.3934	-43.1964	-17.7045	9.9617
14	2.7703	1.7396	0.2858	2.261	0.2999	3.9326	0.0916	0.0034	0.3138	-0.3187	-0.2406	-0.2836	-0.1821	0.3914	0.0418	0.2685	-0.1117	-0.0055	0.4029	0.1091	0.3067	-17.5056	17.1274	8.8477
15	3.7024	0.5271	-3.4437	2.1435	-0.4818	5.6306	0.477	0.6126	0.8216	1.1145	-0.0638	0.8143	-0.9267	-1.3161	0.1082	0.5358	0.008	0.0545	0.4299	0.0676	0.4662	-32.3454	20.897	6.9204
16	1.4596	0.1541	-2.083	1.7998	-0.4399	2.7963	0.1948	-0.1251	-0.3504	0.1907	-0.1401	-0.1824	0.3241	0.579	0.1027	0.3435	-0.0131	-0.079	0.3152	0.0385	0.3251	-22.1622	-3.2399	11.2915
17	1.9196	1.5015	0.3447	1.9802	-0.2453	4.762	-0.0033	-0.0387	-0.2378	-0.0209	0.0971	0.1954	0.2811	-0.1506	0.0652	0.2995	0.0032	-0.0576	0.2687	0.0597	0.2622	-27.0595	-7.7652	9.5978
18	3.0182	-0.6382	0.8477	2.3061	0.296	3.7403	0.0368	-0.3074	-0.2748	0.6573	-0.015	-0.0518	0.3109	-0.1384	0.0656	0.4475	-0.0216	-0.0001	0.5168	0.0508	0.3009	-23.3977	-3.8649	26.8675
19	1.9894	1.4044	-0.35	1.3224	-1.2908	2.8663	0.0109	-0.227	0.1573	0.3329	-0.0347	-0.2354	-0.4075	0.5539	0.0473	0.385	-0.0375	-0.089	0.4704	0.0325	0.2475	-16.9623	5.2965	20.609
20	2.1676	-1.3471	-1.7177	1.9692	-0.6032	3.3689	-0.0514	-0.1423	0.2427	0.3556	0.2264	-0.0404	-0.5745	-0.3839	-0.0579	0.2846	-0.0149	-0.0009	0.3136	0.0212	0.2219	-31.0916	16.4071	17.0592
21	2.4641	0.0877	1.1929	2.4511	-2.052	4.436	-0.0458	0.4855	-0.2907	-0.5179	-0.3868	0.6738	1.1588	-0.3862	-0.2323	0.624	-0.391	0.005	0.6142	-0.1582	0.4121	-45.9436	-17.2967	-13.0701
22	1.3043	0.4931	-0.0099	0.8392	-0.5793	2.0232	0.2999	0.6669	0.0226	-0.3037	-0.1544	0.659	0.07	-1.4965	-0.083	0.3767	-0.0044	-0.0749	0.844	0.028	0.3912	-51.0626	-2.0916	-12.3986
23	2.1783	-0.2716	-1.0288	1.4319	0.7364	3.2576	-0.1488	0.3125	-0.6319	0.0673	0.0122	0.0329	0.7359	-0.1308	0.0916	0.476	-0.0322	0.0155	0.2874	-0.0413	0.2892	-26.049	-9.9364	-14.2921
24	1.9237	1.0476	-0.2604	2.6926	-0.0473	5.9278	-0.4659	0.2896	0.2512	-0.1534	-0.0617	-0.1522	-0.3695	-0.1352	0.0903	0.2697	0.0158	0.0246	0.2665	-0.0599	0.2371	-26.4865	-4.1068	-12.1606
25	1.3187	0.2425	-0.5305	2.229	-0.4053	2.7944	-0.0316	0.315	0.1191	-0.5878	-0.2662	-0.2748	0.3816	0.1521	0.0079	0.374	0.0598	0.0512	0.2959	-0.0497	0.2952	-21.4805	-6.7165	-22.1367
26	4.4586	-0.6355	0.091	2.3571	-0.7928	2.4347	-0.2399	1.1118	-0.8653	-1.0987	0.3066	0.0349	0.3837	0.1774	0.2395	0.8696	0.1696	0.0405	0.5832	-0.1598	0.323	-23.9272	-12.883	-32.7898
27	0.2318	0.1553	-0.6983	1.1818	-0.8581	1.7391	-0.3171	1.0556	-1.0485	-0.0794	0.0422	-0.0999	1.2919	-0.5976	-0.02	0.6963	-0.1187	0.0341	0.5868	-0.1583	0.4144	-30.3866	-16.8394	-23.9983
28	2.0396	0.0639	-0.1752	1.0452	0.0131	1.2601	0.1627	0.656	0.2285	-0.4062	0.1479	0.4459	0.5182	-1.0512	0.0279	0.4262	-0.1224	-0.066	0.7591	0.02	0.4051	-46.2762	-3.6266	-21.4731

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 17 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 37 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 38 through 56 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 57 through 85 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 86 through 139 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 140 through 152 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 153 through 179 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 180 through 216 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 4 through 37 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 38 through 70 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 71 through 87 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 88 through 165 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 166 through 217 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 6 through 17 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 18 through 37 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 38 through 70 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 71 through 99 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 100 through 155 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 156 through 179 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 180 through 217 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 4 through 17 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 18 through 37 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 38 through 70 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 71 through 85 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 86 through 139 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 140 through 152 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 153 through 179 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 180 through 217 )

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