PDB-8rib: N-terminal domain of Trypanosoma brucei PEX14 in complex with a p...

ID or keywords:

Entry

Database: PDB / ID: 8rib

Title

N-terminal domain of Trypanosoma brucei PEX14 in complex with a pyrazolo-pyrazolo[4,3-c]pyridin-3-yl compound showing a novel binding pose

Components

Peroxisomal membrane protein PEX14

Keywords

SIGNALING PROTEIN / Structure-based drug discovery / Complex / Inhibitor / Trypanosomiasis

Function / homology

Function and homology information

glycosome membrane / peroxisomal importomer complex / protein import into peroxisome matrix, docking / protein targeting to vacuole / glycosome / post-transcriptional regulation of gene expression / signaling receptor binding
Similarity search - Function

Biological species

Trypanosoma brucei brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.126 Å

Authors

Napolitano, V. / Janna Olmos, J. / Popowicz, G.M. / Dubin, G.

Funding support

Poland, 1items

Citation

Journal: To Be Published
Title: Quantum Chemistry in a Pocket
Authors: Menezes, F. / Napolitano, V. / Frohlich, T. / Rioton, S. / Janna Olmos, J.D. / Dubin, G. / Popowicz, G.M.

History

Deposition	Dec 18, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 29, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8rib.cif.gz	132.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8rib.ent.gz	102.5 KB	Display	PDB format
PDBx/mmJSON format	8rib.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8rib_validation.pdf.gz	955.8 KB	Display	wwPDB validaton report
Full document	8rib_full_validation.pdf.gz	960.1 KB	Display
Data in XML	8rib_validation.xml.gz	12.8 KB	Display
Data in CIF	8rib_validation.cif.gz	16.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ri/8rib ftp://data.pdbj.org/pub/pdb/validation_reports/ri/8rib	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: Peroxisomal membrane protein PEX14

B: Peroxisomal membrane protein PEX14

hetero molecules

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

1

A: Peroxisomal membrane protein PEX14

hetero molecules

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

2

B: Peroxisomal membrane protein PEX14

hetero molecules

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

Unit cell

Length a, b, c (Å)	56.009, 45.742, 52.616
Angle α, β, γ (deg.)	90.000, 118.868, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-103- EDO
2	1	A-264- HOH
3	1	B-269- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 5 - 66 / Label seq-ID: 8 - 69

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Protein , 1 types, 2 molecules AB

#1: Protein	Peroxisomal membrane protein PEX14 / Peroxin-14 Mass: 7959.192 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PEX14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IEW2

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Non-polymers , 6 types, 190 molecules

#2: Chemical	ChemComp-OJN / 1-(2-azanylethyl)-5-[(4-methoxynaphthalen-1-yl)methyl]-~{N}-[(4-methylsulfanylphenyl)methyl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridine-3-carboxamide / 1-(2-azanylethyl)-5-[(4-methoxynaphthalen-1-yl)methyl]-N-[(4-methylsulfanylphenyl)methyl]-6,7-dihydro-4H-pyrazolo[4,3-c]pyridine-3-carboxamide Mass: 515.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₉H₃₃N₅O₂S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C₂H₆O₂
#4: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₂O₄
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 1.87 Å³/Da / Density % sol: 34.29 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2M sodium malonate dibasic monohydrate 20% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 10, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.126→46.08 Å / Num. obs: 35511 / % possible obs: 89.6 % / Redundancy: 5.8 % / CC_1/2: 0.99 / Net I/σ(I): 14.7
Reflection shell	Resolution: 1.126→3.41 Å / Num. unique obs: 1642 / CC_1/2: 0.71

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.126→46.078 Å / Cor.coef. F_o:F_c: 0.985 / Cor.coef. F_o:F_c free: 0.979 / WR_factor R_free: 0.165 / WR_factor R_work: 0.124 / SU B: 1.892 / SU ML: 0.035 / Average fsc free: 0.9081 / Average fsc work: 0.9195 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1619	1664	4.686 %	RANDOM
R_work	0.1264	33847	-	-
all	0.128	-	-	-
obs	-	35511	80.396 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 20.422 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.372 Å²	-0 Å²	-0.527 Å²
2-	-	1.878 Å²	0 Å²
3-	-	-	-0.575 Å²

Refinement step

Cycle: LAST / Resolution: 1.126→46.078 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	990	0	134	172	1296

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	1225
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.014	1237
X-RAY DIFFRACTION	r_angle_refined_deg	1.833	1.68	1637
X-RAY DIFFRACTION	r_angle_other_deg	1.526	1.594	2863
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.315	5	146
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	23.86	19.333	60
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.886	15	237
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	0.001	15	1
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.779	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	150
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1400
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	272
X-RAY DIFFRACTION	r_nbd_refined	0.279	0.2	369
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.209	0.2	1193
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	616
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	549
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.305	0.2	139
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.126	0.2	5
X-RAY DIFFRACTION	r_metal_ion_refined	0.266	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.352	0.2	38
X-RAY DIFFRACTION	r_nbd_other	0.241	0.2	78
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.205	0.2	36
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.522	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	1.243	1.034	545
X-RAY DIFFRACTION	r_mcbond_other	1.214	1.029	544
X-RAY DIFFRACTION	r_mcangle_it	1.597	1.549	695
X-RAY DIFFRACTION	r_mcangle_other	1.597	1.553	696
X-RAY DIFFRACTION	r_scbond_it	2.674	1.445	680
X-RAY DIFFRACTION	r_scbond_other	2.632	1.439	677
X-RAY DIFFRACTION	r_scangle_it	3.014	2.003	939
X-RAY DIFFRACTION	r_scangle_other	3.013	2.006	940
X-RAY DIFFRACTION	r_lrange_it	3.624	16.51	1635
X-RAY DIFFRACTION	r_lrange_other	3.461	15.442	1580
X-RAY DIFFRACTION	r_rigid_bond_restr	2.712	3	2459
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.108	0.05	2154

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.10837	0.05006
1	2	B	X-RAY DIFFRACTION	Local ncs	0.10837	0.05006

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.126-1.155	0.496	17	0.438	410	0.441	3230	0.2	0.179	13.2198	0.375
1.155-1.186	0.301	53	0.377	842	0.372	3171	0.635	0.558	28.2245	0.35
1.186-1.221	0.315	80	0.327	1269	0.326	3103	0.727	0.741	43.4741	0.294
1.221-1.258	0.305	90	0.291	1726	0.291	3010	0.765	0.796	60.3322	0.263
1.258-1.3	0.239	101	0.24	2187	0.24	2889	0.845	0.87	79.197	0.205
1.3-1.345	0.226	116	0.2	2676	0.201	2805	0.902	0.904	99.5365	0.168
1.345-1.396	0.212	125	0.172	2587	0.174	2712	0.914	0.923	100	0.142
1.396-1.453	0.191	133	0.143	2465	0.145	2598	0.942	0.949	100	0.117
1.453-1.517	0.19	107	0.116	2398	0.119	2505	0.948	0.962	100	0.098
1.517-1.591	0.167	119	0.108	2276	0.111	2395	0.961	0.973	100	0.088
1.591-1.677	0.137	109	0.093	2156	0.095	2266	0.975	0.98	99.9559	0.08
1.677-1.779	0.16	107	0.099	2054	0.102	2161	0.971	0.978	100	0.088
1.779-1.902	0.162	82	0.099	1980	0.101	2062	0.965	0.978	100	0.093
1.902-2.054	0.141	70	0.094	1812	0.096	1882	0.971	0.982	100	0.095
2.054-2.249	0.151	80	0.092	1672	0.095	1752	0.974	0.984	100	0.1
2.249-2.514	0.152	77	0.106	1476	0.108	1555	0.975	0.98	99.8714	0.119
2.514-2.901	0.156	77	0.122	1330	0.124	1407	0.965	0.974	100	0.144
2.901-3.55	0.16	66	0.119	1126	0.121	1193	0.967	0.978	99.9162	0.147
3.55-5.005	0.125	43	0.109	883	0.11	929	0.984	0.984	99.6771	0.145
5.005-46.078	0.154	11	0.195	522	0.194	535	0.928	0.959	99.6262	0.258

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	2.3129	-0.3865	0.2324	2.9246	-0.2015	1.9508	0.0456	-0.1385	-0.034	0.2122	-0.0037	0.0118	0.0847	-0.0472	-0.0419	0.0395	-0.0193	0.0014	0.0188	0.0001	0.002	12.4478	11.7174	10.4616
2	3.085	-0.2916	0.7514	3.4213	-0.0715	1.9609	0.072	0.2811	0.1278	-0.1886	-0.0744	-0.0317	-0.0411	0.1014	0.0024	0.0366	0.0263	0.0189	0.0431	0.0212	0.015	10.1549	9.6997	-10.5171

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	5 - 66
2	X-RAY DIFFRACTION	1	ALL	A	101
3	X-RAY DIFFRACTION	1	ALL	A	102
4	X-RAY DIFFRACTION	1	ALL	A	103
5	X-RAY DIFFRACTION	1	ALL	A	104
6	X-RAY DIFFRACTION	1	ALL	A	105
7	X-RAY DIFFRACTION	1	ALL	A	107
8	X-RAY DIFFRACTION	1	ALL	A	108
9	X-RAY DIFFRACTION	2	ALL	B	5 - 66
10	X-RAY DIFFRACTION	2	ALL	B	101
11	X-RAY DIFFRACTION	2	ALL	B	102
12	X-RAY DIFFRACTION	2	ALL	B	103
13	X-RAY DIFFRACTION	2	ALL	B	108
14	X-RAY DIFFRACTION	2	ALL	B	109

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