PDB-8tr1: Crystal structure of trypanosome brucei hypoxanthine guanine phos...

ID or keywords:

Entry

Database: PDB / ID: 8tr1

Title

Crystal structure of trypanosome brucei hypoxanthine guanine phosphopribosyltransferase in complex with [2S,4R]-4-Guanin-9-yl-2-(2- phosphonoethoxymethyl)-1-N-(3-phosphonopropionyl)pyrrolidine

Components

Hypoxanthine-guanine phosphoribosyltransferase

Keywords

TRANSFERASE /

INHIBITOR /

COMPLEX / PURINE BASE

Function / homology

Function and homology information

hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity /

hypoxanthine phosphoribosyltransferase activity / IMP salvage /

glycosome / nuclear lumen / ciliary plasm / purine ribonucleoside salvage /

nucleotide binding /

metal ion binding ...
Similarity search - Function

Biological species

Trypanosoma brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.46 Å

Authors

Guddat, L.W.

Funding support

Australia, 1items

Citation

Journal: J.Med.Chem. / Year: 2024
Title: Development of Prolinol Containing Inhibitors of Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase: Rational Structure-Based Drug Design.
Authors: Keough, D.T. / Petrova, M. / King, G. / Kratochvil, M. / Pohl, R. / Dolezelova, E. / Zikova, A. / Guddat, L.W. / Rejman, D.

History

Deposition	Aug 9, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2024	Provider: repository / Type: Initial release
Revision 1.1	May 22, 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

-
Download

PDBx/mmCIF format	8tr1.cif.gz	365.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8tr1.ent.gz	248.9 KB	Display	PDB format
PDBx/mmJSON format	8tr1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tr/8tr1 ftp://data.pdbj.org/pub/pdb/validation_reports/tr/8tr1	HTTPS FTP

-
Related structure data

Related structure data	8tpvC 8tpyC 8ts4C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (6)

Deposited unit

A: Hypoxanthine-guanine phosphoribosyltransferase

B: Hypoxanthine-guanine phosphoribosyltransferase

C: Hypoxanthine-guanine phosphoribosyltransferase

D: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

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

1

A: Hypoxanthine-guanine phosphoribosyltransferase

B: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

defined by author&software
Evidence: equilibrium centrifugation, A and B are one dimer C and D the other dimer
45.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Hypoxanthine-guanine phosphoribosyltransferase

D: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	56.862, 88.278, 94.314
Angle α, β, γ (deg.)	90.000, 106.050, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Hypoxanthine-guanine phosphoribosyltransferase / Mass: 22420.771 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: HGPRT / Production host: Escherichia coli (E. coli) / References: UniProt: Q07010
#2: Chemical	ChemComp-JEI / (3-{(2S,4R)-4-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-[(2-phosphonoethoxy)methyl]pyrrolidin-1-yl}-3-oxopropyl)phosphonic acid Mass: 494.333 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₄N₆O₉P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 56.96 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M MgCl2 , 0.1 M Bis-Tris, pH 5.0, 20% 3350 / PH range: 5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.937 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 11, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.937 Å / Relative weight: 1
Reflection	Resolution: 2.46→46.46 Å / Num. obs: 32198 / % possible obs: 98.45 % / Redundancy: 3.4 % / B_iso Wilson estimate: 27.54 Å² / CC_1/2: 0.95 / Net I/σ(I): 6.5
Reflection shell	Resolution: 2.46→2.53 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2554 / CC_1/2: 0.87 / % possible all: 99

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.46→46.46 Å / SU ML: 0.3863 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.7074
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2869	1703	5.36 %
R_work	0.2295	30061	-
obs	0.2326	31764	97.25 %

Solvent computation

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

Displacement parameters

B_iso mean: 33.38 Å²

Refinement step

Cycle: LAST / Resolution: 2.46→46.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5578	0	128	378	6084

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	5863
X-RAY DIFFRACTION	f_angle_d	0.5765	7975
X-RAY DIFFRACTION	f_chiral_restr	0.0435	925
X-RAY DIFFRACTION	f_plane_restr	0.0038	992
X-RAY DIFFRACTION	f_dihedral_angle_d	9.0017	815

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 (%)
2.46-2.53	0.3671	140	0.3129	2414	X-RAY DIFFRACTION	94.8
2.53-2.61	0.3775	132	0.3002	2490	X-RAY DIFFRACTION	96.22
2.61-2.71	0.3987	138	0.314	2464	X-RAY DIFFRACTION	95.98
2.71-2.82	0.394	143	0.2924	2454	X-RAY DIFFRACTION	96.22
2.82-2.94	0.3247	142	0.2608	2467	X-RAY DIFFRACTION	96.67
2.94-3.1	0.3479	137	0.2644	2482	X-RAY DIFFRACTION	96.39
3.1-3.29	0.2994	142	0.2437	2479	X-RAY DIFFRACTION	96.36
3.29-3.55	0.2396	148	0.2157	2531	X-RAY DIFFRACTION	98.71
3.55-3.9	0.2746	142	0.1949	2540	X-RAY DIFFRACTION	99.11
3.91-4.47	0.2396	151	0.1748	2562	X-RAY DIFFRACTION	99.16
4.47-5.63	0.2205	142	0.1875	2580	X-RAY DIFFRACTION	99.09
5.63-46.46	0.2677	146	0.2259	2598	X-RAY DIFFRACTION	98.25

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	1.02397509347	-0.159734411906	-0.204455726921	1.69919953579	-0.587608985272	4.21489125162	-0.0165310774665	-0.267893053019	-0.663432302093	-0.242126928901	-0.123664769618	-0.247187368449	0.323363158187	0.0661348259766	0.159233072634	0.313661445273	0.0524228102456	0.0918971962552	0.247906607644	0.0296268420319	0.246978138839	19.8643176191	17.376986249	-54.7812460888
2	1.24111586212	0.325092073718	-0.56611118218	2.408091453	-0.71974609953	4.12101651228	0.0422484421611	-0.0337216983661	-0.197144481206	0.11876193779	-0.187039486829	-0.134211484894	-0.451616187401	0.777187075185	0.192657449061	0.274118750932	-0.0267389585991	0.00744212191669	0.264238381184	0.00902671690518	0.219935400057	26.2396362961	28.8485406852	-42.9898403317
3	0.91640929805	0.0227688496188	-0.698126167047	0.442801307345	-0.538091721301	3.14755326715	0.309528279274	-0.344760011933	0.143138586065	0.19723943818	-0.185125700345	-0.0165136780192	-0.859043568773	0.523532191039	0.082773124768	0.323232108365	-0.172942209432	-0.0275535591684	0.330539476681	0.0101438274977	0.334390485432	25.5082646375	34.7864506198	-46.929968675
4	2.20553248081	-0.356301491575	-1.88802769019	1.2059850525	0.790794759875	3.2471015462	0.0768471641958	-0.284875479553	1.18005175762	0.625947884913	0.0958462545405	0.0929846806747	-1.29140050902	0.733121021224	0.114894689023	0.639189859238	-0.0808004661603	0.00809836512361	0.312817637694	0.0282095556307	0.462843795678	27.5896105213	42.8150656206	-54.5924182456
5	2.33903683969	-0.397347710087	-0.271765746799	1.86409791228	-1.07193588311	2.34068273376	0.0343099690153	-0.0144084251122	0.0993027559353	-0.0523354821083	-0.287005066934	-0.22108481758	-0.0774430380739	0.615472752207	0.0913352155021	0.264749563128	-0.0733639265487	-0.0160302993442	0.233583894648	-0.00976331193337	0.17294077843	25.505271326	30.3045421489	-59.8325985852
6	2.76044544111	0.140510951272	-0.876975924656	1.91598380531	-1.1465796159	3.69034216295	-0.0796122841146	0.564765214705	0.060969832786	0.093419544608	-0.223429663255	0.316025100039	-0.0670877081151	-0.51599594456	-0.049606169287	0.283560326727	0.0106552359386	-0.0224015302836	0.283195269023	-0.0647782764099	0.27407460019	8.19189748722	24.3381875013	-57.3393881699
7	8.25785073527	-1.74059387378	-1.80000684946	4.28558147166	2.44102925141	6.0921195691	1.16636927346	1.51997595499	0.302307107158	-1.09513430808	-1.16656929629	0.863482819679	-0.480615044648	-2.04685404184	0.0767819896417	0.576608251423	0.108642595592	-0.106895078152	0.828706180411	0.0235494675872	0.449553633491	-5.27594403428	30.3186972957	-66.1077019786
8	8.84953307617	3.94467970657	3.2678235188	4.35049540878	-1.54837280799	4.72340509844	0.169281990919	-0.612077820722	1.21345311142	-0.458207696559	0.192269520344	0.455183039461	-0.642160827199	-0.919240444774	-0.360848479787	0.371695085437	0.069759444002	0.0210387627049	0.260759169492	-0.0581206814619	0.320788108987	-12.2550816207	24.7275225838	11.5752837255
9	2.25907218879	-0.368826360524	-0.645378247486	1.88453987746	0.701754989556	2.4173198806	0.124941301271	-0.113719426744	-0.0392289067881	0.0614002244475	-0.0491122702568	-0.0557372745438	-0.200428165503	0.280973816922	0.00895076267236	0.276742776394	-0.00854895213716	0.00204944891726	0.202334587015	0.0103529657767	0.215349827783	11.5913701635	15.6703875667	7.50847943678
10	2.89543764481	1.24216504783	0.0616944950808	0.612193085702	-0.152116684883	1.53909458292	-0.279846033376	0.195349842931	-0.551126937208	-0.187340610364	0.0178487629682	-0.11984898971	0.683329126705	0.0548012045114	0.14298988971	0.478501811631	0.0348926785685	0.0960185741596	0.276650859871	0.023309271097	0.356695758536	13.0049193784	3.81565710383	3.96401403208
11	4.07278729461	-0.587837781472	-1.31104767232	2.04297686517	0.0701986088023	1.93449293739	-0.133215718524	-0.212813716035	-0.244434921855	0.268336543763	0.00113659440441	-0.0482905412547	0.325722412691	0.110907578689	0.173752018051	0.354444618845	0.0205089460815	-0.0110272505701	0.164351331576	0.00789182034936	0.243919421942	6.91685291978	4.63847097377	15.6875019637
12	1.45695831704	-0.375054065242	0.22142368955	0.608258540892	0.500473724793	1.73649888152	-0.0349691964453	-0.0516513208775	-0.0861931077306	0.0667946149782	-0.0109803551683	0.141873724738	-0.164836786886	-0.17533100123	0.0528817807288	0.329596193369	0.0035641685122	0.059715491489	0.205235029184	0.0188936228126	0.250203083954	-5.40844527101	13.7829945706	13.9265024811
13	6.9538260665	2.97029292466	1.65850855869	4.92368705674	2.7910641664	8.99919593906	0.117529857553	-0.410582120177	-0.750204073807	0.57859886566	-0.516781469061	0.241577820919	0.884013454891	-0.322677201593	0.306195632588	0.230023690768	0.0308068764521	0.0407365001723	0.554776981868	0.0229267794428	0.538827198648	-24.1002201801	7.14785766569	10.8288998438
14	3.21337519335	0.224030990528	-0.74191606055	1.59409985929	-0.428127448384	2.673613868	0.0894853523005	0.171680617941	0.155675588058	0.039324622157	-0.0805852267367	0.102408030867	-0.47977022147	-0.355458862715	-0.0210776681584	0.330372791719	0.0528608356211	0.0388053321729	0.191574755221	-0.0340975464313	0.196746834195	-2.98160090769	18.4446817702	-8.10345337669
15	4.36290608572	0.86038772609	1.1531555647	0.158650102976	0.208943836561	3.78339989666	0.0809829317599	-0.223839754842	-0.399100081756	0.196260391946	-0.0590805963357	-0.0563353841221	0.427243293181	-0.166364733777	0.0199772980322	0.256340459056	0.0207493604139	0.0611262399681	0.297979359663	-0.110412432902	0.380796148349	-11.247241673	7.19268171491	-4.30970034053
16	2.62034451304	0.282464847155	-0.32542366607	0.998381079476	-0.437834727905	2.71544732772	-0.0579831164604	0.457849169095	-0.189949109994	-0.145580440719	-0.0147104689119	-0.0466641608571	0.0277894324264	-0.119461869077	0.0989853580137	0.195459187534	0.00948012287467	0.0122547244357	0.168421835441	-0.0379027012924	0.222510135023	0.0726153380733	8.48688649668	-15.8442363242
17	0.306133040146	0.182065614744	0.067825518542	0.900330141441	-0.243576041995	0.842893002977	-0.0250322576049	-0.0171678025498	-0.143636175685	-0.0121831040867	-0.205894734214	-0.384892866288	0.344813971578	0.391909136454	0.0298886345017	0.313662409897	0.0352744206586	0.0519304760121	0.274872331198	0.0565269992215	0.321280683276	17.5539811073	11.5460152415	-10.8061987549
18	2.65368508447	0.153212171755	0.193344515958	0.888531427854	0.0821944758855	3.63704380539	-0.00416243732586	0.17137617045	-0.10362136084	0.0281821665503	-0.0536719884903	0.183393796375	-0.0160501673399	-0.280517548358	0.0552959617733	0.23748492231	0.00817066094609	0.0254794664313	0.174871507942	-0.0387305083332	0.215056214611	4.93048060538	24.1934623017	-41.5818315362
19	0.649264671934	-0.0509822131153	-0.217418591651	1.14339422863	-0.398320439345	2.82140363104	-0.0404305508507	-0.0651628366243	0.161245641509	0.214367571514	-0.0463045794839	0.0957567680953	-0.353564259862	-0.211593815113	0.0991857504699	0.353532097901	0.00783306983011	0.00233583733577	0.210297583578	-0.0110916306764	0.22892590572	5.11695440194	31.8989818456	-32.1204940907
20	6.08970673839	6.58808551054	1.5513772539	7.1695369538	1.67931461339	0.395238856731	0.865213636341	-1.80975033039	0.256416918245	1.39424432658	-1.05136705114	0.0189322994775	-0.113402106412	0.393152120593	-0.00862702197736	0.584602791128	-0.241673057058	-0.103215620244	0.548888143133	-0.0163731507073	0.409711882185	26.1079723844	30.851619908	-24.4162887218

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'D' and (resid 5 through 34 )	D	G	5 - 34	1 - 30
2	2	chain 'D' and (resid 35 through 69 )	D	G	35 - 69	31 - 65
3	3	chain 'D' and (resid 70 through 119 )	D	G	70 - 119	66 - 94
4	4	chain 'D' and (resid 120 through 132 )	D	G	120 - 132	95 - 107
5	5	chain 'D' and (resid 133 through 168 )	D	G	133 - 168	108 - 143
6	6	chain 'D' and (resid 169 through 188 )	D	G	169 - 188	144 - 163
7	7	chain 'D' and (resid 189 through 204 )	D	G	189 - 204	164 - 179
8	8	chain 'A' and (resid 4 through 16 )	A	A	4 - 16	1 - 13
9	9	chain 'A' and (resid 17 through 70 )	A	A	17 - 70	14 - 67
10	10	chain 'A' and (resid 71 through 107 )	A	A	71 - 107	68 - 83
11	11	chain 'A' and (resid 108 through 148 )	A	A	108 - 148	84 - 124
12	12	chain 'A' and (resid 149 through 188 )	A	A	149 - 188	125 - 164
13	13	chain 'A' and (resid 189 through 202 )	A	A	189 - 202	165 - 178
14	14	chain 'B' and (resid 5 through 69 )	B	C	5 - 69	1 - 65
15	15	chain 'B' and (resid 70 through 107 )	B	C	70 - 107	66 - 83
16	16	chain 'B' and (resid 108 through 178 )	B	C	108 - 178	84 - 154
17	17	chain 'B' and (resid 179 through 198 )	B	C - D	179 - 301	155
18	18	chain 'C' and (resid 5 through 107 )	C	E	5 - 107	1 - 82
19	19	chain 'C' and (resid 108 through 181 )	C	E	108 - 181	83 - 156
20	20	chain 'C' and (resid 182 through 200 )	C	E	182 - 200	157 - 175

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-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

-
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