PDB-5bsk: Human HGPRT in complex with (S)-HPEPG, an acyclic nucleoside phos...

ID or keywords:

Entry

Database: PDB / ID: 5bsk

Title

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

Components

Hypoxanthine-guanine phosphoribosyltransferase

Keywords

TRANSFERASE/TRANSFERASE Inhibitor / Hypoxanthine-guanine-phosphoribosyltransferase /

malaria /

acyclic nucleoside phosphonates / inhibitors / 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 metabolic process / hypoxanthine salvage / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / lymphocyte proliferation /

hypoxanthine phosphoribosyltransferase ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.61 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	Jun 2, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 23, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 30, 2015	Group: Database references
Revision 1.2	Oct 7, 2015	Group: Database references
Revision 1.3	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 / refine / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _refine.pdbx_method_to_determine_struct / _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	5bsk.cif.gz	316.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5bsk.ent.gz	259.5 KB	Display	PDB format
PDBx/mmJSON format	5bsk.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/bs/5bsk ftp://data.pdbj.org/pub/pdb/validation_reports/bs/5bsk	HTTPS FTP

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Related structure data

Related structure data	5brnC 4ijqS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6bnj-d 5fp1-d 1z7g-2 1qkc-d 5brn-d 5nec-2 5nec-1 6dxp-d 4rao-d 1qjq-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

99.5 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)	74.272, 93.279, 129.881
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-4X7 / (2-{[(2S)-1-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3-hydroxypropan-2-yl]oxy}ethyl)phosphonic acid Mass: 333.238 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₆P
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.28 Å³/Da / Density % sol: 46.17 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 15% PEG 3000, 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: Jun 22, 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: 2.61→46.64 Å / Num. obs: 27248 / % possible obs: 97.3 % / Redundancy: 5.6 % / R_merge(I) obs: 0.12 / Net I/σ(I): 10.4

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4IJQ

4ijq

Resolution: 2.61→46.64 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.57 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.268	2000	7.35 %
R_work	0.206	-	-
obs	0.21	27197	96.7 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.61→46.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5953	0	92	121	6166

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6272
X-RAY DIFFRACTION	f_angle_d	0.67	8516
X-RAY DIFFRACTION	f_dihedral_angle_d	12.575	2310
X-RAY DIFFRACTION	f_chiral_restr	0.02	966
X-RAY DIFFRACTION	f_plane_restr	0.004	1077

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 (%)
2.61-2.6749	0.3621	140	0.2719	1770	X-RAY DIFFRACTION	96
2.6749-2.7473	0.3368	143	0.2632	1805	X-RAY DIFFRACTION	98
2.7473-2.8281	0.3042	143	0.2606	1791	X-RAY DIFFRACTION	98
2.8281-2.9194	0.3864	142	0.2597	1793	X-RAY DIFFRACTION	98
2.9194-3.0237	0.2841	142	0.2369	1795	X-RAY DIFFRACTION	98
3.0237-3.1447	0.287	144	0.2312	1815	X-RAY DIFFRACTION	98
3.1447-3.2878	0.2881	142	0.2236	1780	X-RAY DIFFRACTION	98
3.2878-3.4611	0.295	143	0.2173	1811	X-RAY DIFFRACTION	97
3.4611-3.6779	0.2681	141	0.2028	1785	X-RAY DIFFRACTION	97
3.6779-3.9617	0.2424	144	0.1868	1798	X-RAY DIFFRACTION	97
3.9617-4.3601	0.1997	142	0.1682	1806	X-RAY DIFFRACTION	96
4.3601-4.9904	0.2198	144	0.1604	1808	X-RAY DIFFRACTION	96
4.9904-6.2849	0.2517	144	0.1959	1814	X-RAY DIFFRACTION	95
6.2849-46.6469	0.2785	146	0.1983	1826	X-RAY DIFFRACTION	92

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	5.7706	-6.0169	4.3448	9.1706	-7.9313	7.348	0.1165	-0.5282	-0.3361	0.599	-0.8308	-1.4419	-0.5867	1.9168	0.7423	0.4123	-0.0632	-0.0071	0.9465	-0.0903	0.4532	18.3298	-33.0934	-14.5009
2	1.746	-0.745	-1.0222	2.1066	0.1556	1.7894	-0.1509	0.1084	0.0749	0.0162	0.2841	-0.3484	-0.1515	0.3036	-0.1919	0.2385	-0.061	-0.0548	0.4258	0.0263	0.1992	8.4505	-30.5399	-20.2916
3	6.704	-0.1966	-1.127	3.787	-1.5587	9.8113	-0.3511	-0.2405	-0.5061	0.1798	0.2609	0.1188	0.033	-0.4246	0.1922	0.1678	0.007	0.0185	0.2902	0.0388	0.3335	-5.5422	-41.4931	-18.6343
4	2.6405	0.157	-0.2548	3.8107	-0.4362	3.0224	0.0399	-0.6634	-0.0619	0.7967	-0.0145	0.2154	0.0553	0.014	-0.0313	0.3376	0.0021	0.0142	0.4614	0.0235	0.2271	0.5532	-35.1373	-8.8229
5	5.6101	4.7556	5.4247	5.0609	3.5259	7.5952	0.4828	-0.5907	-0.6257	-0.6165	-0.904	1.6634	-0.2827	-1.3998	0.4978	0.354	0.0607	-0.0542	0.8592	0.0138	0.4238	-18.1326	-31.3279	-50.5401
6	3.4042	-1.9828	-1.2108	6.439	0.002	2.4857	-0.0454	0.0067	-0.1802	-0.0702	0.1331	0.3175	-0.1079	-0.0317	-0.057	0.1899	-0.06	-0.0551	0.2356	-0.0421	0.1453	-7.758	-30.336	-45.0216
7	4.2128	-0.3943	-1.4904	4.811	0.0847	8.3601	-0.1131	-0.0874	-0.1165	-0.3724	-0.421	-0.1998	-0.0267	0.7197	0.4351	0.2077	0.0013	0.0267	0.3053	-0.027	0.2306	5.1779	-41.6937	-46.5848
8	3.9853	-2.8566	1.1216	5.1756	-1.4576	3.289	0.1717	0.5108	-0.1288	-0.6554	-0.1991	-0.2862	0.2858	0.3084	0.0103	0.3153	-0.0127	0.0269	0.3289	-0.0608	0.2509	1.9795	-41.7429	-58.8266
9	6.2694	2.9961	-0.0068	9.4468	-0.0583	3.8069	0.1261	0.5369	0.1798	-0.4342	-0.2261	-0.2078	-0.3383	0.0465	0.0806	0.2149	0.0644	0.0267	0.252	-0.0067	0.1751	-4.9818	-21.0414	-52.9427
10	2.0894	-9.7365	0.5905	9.8337	-1.3798	0.9811	0.8441	0.6119	-0.4431	-1.2529	-0.8559	0.6057	-0.2359	-0.728	0.1122	0.3343	-0.0299	-0.0149	0.59	-0.0441	0.4007	-24.0983	-32.205	-41.6005
11	0.5408	-0.3888	-0.3997	7.2494	-0.8316	2.338	-0.0889	0.0831	-0.0895	-0.3952	0.2004	-0.0052	0.0195	-0.1507	-0.1325	0.1579	-0.0087	-0.0105	0.3682	-0.0577	0.181	-14.4056	-34.1769	-34.7758
12	3.7494	-0.8818	1.7802	9.0229	3.5342	4.2143	-0.1797	-0.0465	-0.2673	-0.1895	0.1245	0.2983	-0.4071	0.3049	0.0906	0.4195	0.0019	0.0786	0.3478	-0.0106	0.2971	-14.1442	-21.7297	-17.2148
13	5.5831	-1.4708	-1.4658	2.6809	1.2752	8.91	-0.1111	0.0011	-0.0183	0.0058	0.1397	-0.074	0.1439	0.5815	-0.0556	0.2073	0.0428	-0.0423	0.2589	-0.0139	0.1893	-7.4295	-23.0037	-21.0766
14	1.0263	-0.3774	-0.274	3.115	0.6921	1.0414	0.0271	-0.263	-0.0983	0.3335	-0.1002	0.3146	-0.0171	-0.3478	0.0897	0.2444	-0.0063	0.0058	0.4658	0.0024	0.2591	-23.0793	-29.0624	-23.2377
15	5.1873	-1.4654	3.1634	4.5085	-0.4523	2.3693	-0.1943	-0.1804	-1.0461	0.1508	0.3914	0.8729	0.8154	-1.2639	-0.0751	0.605	-0.299	0.0658	0.6112	0.0597	0.7607	-24.7306	-52.0665	-27.1584
16	4.0523	1.9752	-0.6839	4.8167	-0.028	4.0349	0.1335	-0.5818	-0.0054	0.75	-0.137	-0.5703	0.3317	0.2089	0.017	0.2853	0.0496	-0.0436	0.3916	0.0076	0.3252	19.2492	-41.8083	-26.362
17	5.1343	1.6746	0.1141	4.7384	-3.2217	9.0453	0.1175	-0.0198	-0.1915	0.1178	0.1007	-0.335	-0.1403	0.0745	-0.2299	0.1792	0.0311	-0.0117	0.2579	-0.023	0.2426	14.1389	-22.8087	-38.8162
18	4.2987	-0.6662	1.7055	3.6144	-1.3213	2.7637	0.1424	0.3085	-0.1399	-0.517	-0.1591	0.092	-0.0784	0.0255	-0.0013	0.2769	-0.0078	-0.0416	0.3641	0.0009	0.1588	12.9406	-23.2941	-45.2915
19	1.1798	0.4962	0.2308	4.3198	-1.07	1.6557	0.0312	0.3916	0.0734	-0.4783	-0.1151	-0.5198	-0.029	0.5918	0.0707	0.2693	-0.026	0.0192	0.4944	0.0165	0.3648	23.8002	-34.4417	-40.3628

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 4:17 )	A	4 - 17
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 18:55 )	A	18 - 55
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 56:87 )	A	56 - 87
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 88:217 )	A	88 - 217
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 5:17 )	B	5 - 17
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 18:56 )	B	18 - 56
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 57:88 )	B	57 - 88
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 89:179 )	B	89 - 179
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 180:217 )	B	180 - 217
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 4:17 )	C	4 - 17
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 18:55 )	C	18 - 55
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 56:70 )	C	56 - 70
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 71:100 )	C	71 - 100
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 101:208 )	C	101 - 208
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 209:216 )	C	209 - 216
16	X-RAY DIFFRACTION	16	( CHAIN D AND RESID 5:37 )	D	5 - 37
17	X-RAY DIFFRACTION	17	( CHAIN D AND RESID 38:70 )	D	38 - 70
18	X-RAY DIFFRACTION	18	( CHAIN D AND RESID 71:139 )	D	71 - 139
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 140:216 )	D	140 - 216

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