PDB-9ogv: Identification of ligands for E3 ligases using fragment-based methods

ID or keywords:

Entry

Database: PDB / ID: 9ogv

Title

Identification of ligands for E3 ligases using fragment-based methods

Components

TNF receptor-associated factor 4

Keywords

LIGASE / small molecule complex crystal structure / TRAF4 / E3 ligase

Function / homology

Function and homology information

respiratory tube development / respiratory gaseous exchange by respiratory system / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / WW domain binding / positive regulation of protein kinase activity / bicellular tight junction / signaling adaptor activity / positive regulation of JNK cascade ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Phan, J. / Fesik, S.W.

Funding support

1items

Citation

Journal: Rsc Chem Biol / Year: 2025
Title: Identification of ligands for E3 ligases with restricted expression using fragment-based methods.
Authors: Waterson, A.G. / Lehmann, B.D. / Lu, Z. / Sensintaffar, J.L. / Olejniczak, E.T. / Zhao, B. / Rietz, T. / Payne, W.G. / Phan, J. / Fesik, S.W.

History

Deposition	May 2, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 22, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ogv.cif.gz	214.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9ogv.ent.gz		Display	PDB format
PDBx/mmJSON format	9ogv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ogv_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	9ogv_full_validation.pdf.gz	1 MB	Display
Data in XML	9ogv_validation.xml.gz	22.7 KB	Display
Data in CIF	9ogv_validation.cif.gz	28.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/og/9ogv ftp://data.pdbj.org/pub/pdb/validation_reports/og/9ogv	HTTPS FTP

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Related structure data

Related structure data	9ogwC 9olbC C: citing same article (ref.)
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
Related items in Molecule of the Month	#163 - Jul 2013 HIV Capsid similarity (2) #56 - Aug 2004 Caspases similarity (1)

Deposited unit

A: TNF receptor-associated factor 4

B: TNF receptor-associated factor 4

C: TNF receptor-associated factor 4

hetero molecules

63.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	68.927, 72.302, 117.709
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	TNF receptor-associated factor 4 / Cysteine-rich domain associated with RING and Traf domains protein 1 / Metastatic lymph node gene ...Cysteine-rich domain associated with RING and Traf domains protein 1 / Metastatic lymph node gene 62 protein / MLN 62 / RING finger protein 83 Mass: 20938.643 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF4, CART1, MLN62, RNF83 / Production host: Escherichia coli (E. coli) References: UniProt: Q9BUZ4, RING-type E3 ubiquitin transferase
#2: Chemical	ChemComp-A1CA9 / N-(1,3-thiazol-2-yl)quinoxaline-6-carboxamide Mass: 256.283 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₂H₈N₄OS / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.32 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 10-15% PEG 3350, 0.1 M Bis-TRIS pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
Detector	Type: MAR CCD 300 mm / Detector: CCD / Date: Feb 12, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.54→36.4 Å / Num. obs: 17251 / % possible obs: 97.8 % / Redundancy: 8.4 % / CC_1/2: 0.99 / Net I/σ(I): 7.2
Reflection shell	Resolution: 2.54→2.58 Å / Num. unique obs: 1094 / CC_1/2: 0.36

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
PDB_EXTRACT		data extraction
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.8→29.43 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2946	1434	9.99 %
R_work	0.2454	-	-
obs	0.2503	14348	95.51 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.8→29.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4075	0	54	0	4129

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4264
X-RAY DIFFRACTION	f_angle_d	0.676	5781
X-RAY DIFFRACTION	f_dihedral_angle_d	16.035	569
X-RAY DIFFRACTION	f_chiral_restr	0.044	587
X-RAY DIFFRACTION	f_plane_restr	0.004	756

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 (%)
2.8-2.9	0.4176	115	0.3543	1018	X-RAY DIFFRACTION	77
2.9-3.02	0.3905	138	0.3047	1258	X-RAY DIFFRACTION	94
3.02-3.15	0.3056	140	0.2919	1290	X-RAY DIFFRACTION	97
3.15-3.32	0.3116	148	0.2678	1289	X-RAY DIFFRACTION	97
3.32-3.53	0.3081	135	0.2575	1285	X-RAY DIFFRACTION	97
3.53-3.8	0.2963	153	0.2356	1314	X-RAY DIFFRACTION	98
3.8-4.18	0.287	143	0.2223	1332	X-RAY DIFFRACTION	99
4.18-4.78	0.2508	146	0.2031	1339	X-RAY DIFFRACTION	98
4.78-6.02	0.2575	152	0.2178	1373	X-RAY DIFFRACTION	99
6.02-10	0.2823	164	0.2444	1416	X-RAY DIFFRACTION	98

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	0.029	-0.0523	-0.0611	0.1649	0.1435	0.1471	-0.0396	-0.0544	-0.1686	-0.0072	0.1367	0.304	0.0365	-0.3653	-0.0281	0.2998	0.0759	-0.0665	0.5401	0.1395	0.449	-1.4744	86.3027	123.0715
2	0.296	-0.0517	0.0053	0.0956	-0.0416	0.2109	-0.0192	-0.0427	0.0019	-0.1092	-0.0329	-0.0316	0.0156	-0.0973	-0.4951	0.2633	0.0245	0.0317	0.1726	0.0313	0.0892	8.2219	88.7365	132.0515
3	1.0138	-0.4537	-0.0577	1.0545	0.0653	0.5103	0.2037	0.0073	-0.2704	0.253	-0.3524	0.3596	0.1514	-0.0075	-0.1144	-0.0056	-0.0946	0.0338	0.2526	0.1167	0.1884	7.3675	79.1189	135.8873
4	0.5738	-0.2705	-0.1689	0.6288	-0.1156	0.4601	-0.0776	-0.3035	0.0892	0.4214	-0.2441	-0.5617	-0.1106	0.015	-0.0529	0.3068	-0.0432	0.016	0.358	0.0093	0.2045	13.6559	84.5398	140.4447
5	0.002	-0.0024	-0.0025	0.0012	0.0048	0.0028	-0.0035	0.0926	0.1493	0.0883	-0.0865	0.0049	-0.2283	-0.2705	0	0.2536	-0.0115	0.0879	0.5308	-0.1197	0.4644	-2.8786	86.895	110.8899
6	0.8657	0.1828	0.1174	0.531	-0.2492	0.6208	-0.2257	-0.2031	0.117	0.0976	-0.1227	-0.1976	-0.2557	0.0412	-0.3396	0.2248	0.0999	-0.1234	0.0899	0.0508	0.1256	9.3549	78.7847	109.5857
7	0.1608	0.0427	0.047	0.0324	-0.0086	0.0325	-0.0541	0.0159	0.0057	-0.003	0.0424	0.0273	-0.0063	-0.0757	-0.0313	0.4944	-0.4587	0.044	0.4288	-0.2824	0.2078	-2.2534	64.2243	101.9253
8	0.6462	-0.3963	-0.4787	0.5495	0.2928	1.0401	-0.2584	0.1575	0.036	-0.0484	0.0267	0.0801	0.1035	-0.1256	-0.4499	0.1551	-0.0846	-0.0089	0.1481	0.0263	0.1163	6.1606	79.3576	99.6784
9	0.1366	-0.1402	0.2362	0.4695	-0.4039	0.6815	-0.1213	0.2382	0.1665	-0.2198	0.3235	0.1432	0.1377	0.0116	0.3039	0.2013	-0.0752	0.0791	0.3063	-0.0207	0.2561	12.3871	83.1617	97.5178
10	0.5184	0.5055	0.1316	0.558	0.2352	0.2247	0.3443	-0.0841	-0.0715	-0.0167	-0.3032	-0.5093	0.0367	0.2549	0.2688	0.2718	-0.0508	0.1332	0.3695	0.0701	0.3114	19.6165	70.8933	105.1606
11	0.0006	-0.0015	0.0047	0.0101	-0.0007	0.0051	-0.0098	0.0028	-0.0154	-0.0874	-0.0185	0.1059	0.2873	0.254	0.0001	0.7214	-0.1678	-0.0107	0.4736	-0.1007	0.4025	10.7921	89.8489	89.6203
12	0.1249	0.1952	-0.031	0.6728	0.0485	0.0266	-0.1379	0.0952	-0.0621	-0.0393	0.0976	-0.0599	0.2131	0.0019	0.4396	0.4934	-0.1516	0.1562	0.097	-0.0713	0.2868	11.8082	67.2135	103.0123
13	0.0335	-0.0425	0.0936	0.0583	-0.1236	0.2558	0.18	0.0864	0.2498	-0.0824	0.0886	-0.1333	0.0357	-0.0811	0.0171	0.2279	-0.2014	0.1045	1.0291	-0.1177	0.6441	29.5098	96.3011	104.7781
14	0.9557	-0.3622	-0.5974	0.26	0.3843	0.5466	-0.0605	-0.1781	-0.6305	0.2536	-0.1436	0.3196	0.4327	0.0529	-0.0749	0.2345	-0.0261	-0.0799	0.2139	0.0049	0.4282	3.6483	99.1569	114.6459
15	0.6112	0.5486	0.0718	0.5119	0.055	0.4785	-0.1117	0.1021	0.1804	0.0029	-0.0138	0.1087	-0.1247	0.1874	-0.0001	0.1933	0.0242	-0.0227	0.1887	0.0228	0.2201	7.8724	110.1851	114.6431
16	0.3666	-0.357	0.2213	0.3372	-0.1918	0.1209	-0.0476	-0.3664	-0.0063	0.3023	0.112	-0.3167	-0.2638	-0.0262	-0.0162	0.2886	-0.1109	0.089	0.3082	-0.0341	0.3891	11.1204	116.3051	124.4716
17	0.1887	0.0781	-0.2235	0.3248	-0.1267	0.2508	0.1894	-0.0718	-0.2614	-0.2698	-0.1181	0.0233	0.0206	0.2226	0.0235	0.0762	-0.1517	-0.2299	0.2163	0.1039	0.3466	15.1827	108.9323	109.2806

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 291 through 304 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 305 through 316 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 317 through 390 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 391 through 465 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 291 through 301 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 302 through 316 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 317 through 326 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 327 through 358 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 359 through 390 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 391 through 413 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 414 through 423 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 431 through 462 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 463 through 471 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 291 through 316 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 317 through 403 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 404 through 438 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 439 through 472 )

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