PDB-3d6q: The RNase A- 5'-Deoxy-5'-N-piperidinouridine complex

ID or keywords:

Entry

Database: PDB / ID: 3d6q

Title

The RNase A- 5'-Deoxy-5'-N-piperidinouridine complex

Components

Ribonuclease pancreatic

Keywords

HYDROLASE / Ribonuclease A / ligand / Endonuclease / Glycation / Glycoprotein / Nuclease / Secreted

Function / homology

Function and homology information

pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function

Biological species

Bos taurus (cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.6 Å

Authors

Leonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G.

Citation

Journal: J.Med.Chem. / Year: 2009
Title: Morpholino, piperidino, and pyrrolidino derivatives of pyrimidine nucleosides as inhibitors of ribonuclease A: synthesis, biochemical, and crystallographic evaluation.
Authors: Samanta, A. / Leonidas, D.D. / Dasgupta, S. / Pathak, T. / Zographos, S.E. / Oikonomakos, N.G.

History

Deposition	May 20, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 10, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 30, 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 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3d6q.cif.gz	72.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3d6q.ent.gz	54.7 KB	Display	PDB format
PDBx/mmJSON format	3d6q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3d6q_validation.pdf.gz	821.9 KB	Display	wwPDB validaton report
Full document	3d6q_full_validation.pdf.gz	827.3 KB	Display
Data in XML	3d6q_validation.xml.gz	17.1 KB	Display
Data in CIF	3d6q_validation.cif.gz	25.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d6/3d6q ftp://data.pdbj.org/pub/pdb/validation_reports/d6/3d6q	HTTPS FTP

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Related structure data

Related structure data	3d6oC 3d6pC 3d7bC 3d8yC 3d8zC 2g8qS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1o0h-2 4g8v-1 2w5k-2 1fnk-d 6pvx-2 6xhd-2 5uey-d 1rpg-d 1rnc-d 1afk-1 3ev4-1 1rhb-d 1n3z-d 1o0m-2 1qhc-1 1z6d-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#105 - Sep 2008 Ribonuclease A similarity (10) #143 - Nov 2011 Toll-like Receptors similarity (9) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#105 - Sep 2008
Ribonuclease A
similarity (10)
#143 - Nov 2011
Toll-like Receptors
similarity (9)
#129 - Sep 2010
Isocitrate Dehydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#215 - Nov 2017
Aspartate Transcarbamoylase
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)

Deposited unit

A: Ribonuclease pancreatic

B: Ribonuclease pancreatic

hetero molecules

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

1

A: Ribonuclease pancreatic

hetero molecules

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

2

B: Ribonuclease pancreatic

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

Unit cell

Length a, b, c (Å)	100.094, 32.498, 72.496
Angle α, β, γ (deg.)	90.00, 90.71, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-146- HOH
2	1	A-306- HOH

#1: Protein	Ribonuclease pancreatic / RNase 1 / RNase A Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₅O₇
#3: Chemical	ChemComp-U3S / 1-(5-deoxy-5-piperidin-1-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione Mass: 311.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₂₁N₃O₅
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H₂O
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: 2.15 Å³/Da / Density % sol: 42.79 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 4000, SODIUM CITRATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.92 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 1.6→30 Å / Num. all: 31270 / Num. obs: 30942 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / B_iso Wilson estimate: 17.4 Å² / R_sym value: 0.055 / Net I/σ(I): 25.8
Reflection shell	Resolution: 1.6→1.64 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 6.7 / Num. unique all: 1527 / R_sym value: 0.187 / % possible all: 98.2

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
ADSC	Quantum	data collection
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: PDB ENTRY 2G8Q

2g8q

Resolution: 1.6→30 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.944 / SU B: 3.013 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20937	1562	5 %	RANDOM
R_work	0.17861	-	-	-
obs	0.18016	29373	98.93 %	-
all	-	31270	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 16.207 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.08 Å²	0 Å²	-0.03 Å²
2-	-	0.48 Å²	0 Å²
3-	-	-	-0.4 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.096 Å	0.099 Å

Refinement step

Cycle: LAST / Resolution: 1.6→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1902	0	48	369	2319

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.021	1999
X-RAY DIFFRACTION	r_angle_refined_deg	1.443	1.951	2708
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.593	5	246
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.14	25.169	89
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.404	15	339
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.274	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.145	0.2	298
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1505
X-RAY DIFFRACTION	r_nbd_refined	0.186	0.2	947
X-RAY DIFFRACTION	r_nbtor_refined	0.295	0.2	1374
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.127	0.2	305
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.165	0.2	67
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.106	0.2	45
X-RAY DIFFRACTION	r_mcbond_it	0.513	1.5	1273
X-RAY DIFFRACTION	r_mcangle_it	0.879	2	2022
X-RAY DIFFRACTION	r_scbond_it	1.319	3	801
X-RAY DIFFRACTION	r_scangle_it	2.158	4.5	686

LS refinement shell

Resolution: 1.6→1.641 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.254	120	-
R_work	0.206	2120	-
obs	-	-	97.82 %

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	16.0026	2.4745	1.0572	15.0953	7.5705	10.2913	-0.0649	-0.0451	0.7748	-0.6494	0.3206	-0.3655	-1.7691	0.4812	-0.2557	0.2667	-0.0974	0.0794	-0.067	0.03	-0.0201	33.0819	15.1759	12.3871
2	3.5296	-0.6955	-0.0077	3.8318	1.0515	6.1276	0.1723	0.2198	0.0424	-0.1098	-0.032	-0.0573	-0.201	-0.1292	-0.1403	0.0546	0.0075	0.0242	0.0453	0.0426	0.0061	29.2271	5.7837	7.7378
3	3.1845	-0.2125	2.744	0.0142	-0.1831	2.3644	0.9789	0.4569	-0.3852	-0.2775	-0.2313	0.8536	-0.6267	-0.7451	-0.7476	0.513	-0.0768	0.0269	0.3059	-0.0798	0.1921	24.8214	-5.2553	-1.6926
4	3.4927	-0.4901	-2.344	0.8904	0.3491	2.9095	0.1008	0.2882	0.0765	-0.1654	0.0634	-0.1237	-0.1339	-0.0861	-0.1642	0.0363	-0.009	0.0118	0.0637	0.0106	0.0105	32.2213	2.1093	4.7363
5	4.1993	0.0597	0.6925	1.968	-0.6101	2.1543	-0.0306	-0.0319	-0.0719	0.1033	0.048	-0.0849	-0.0302	-0.1844	-0.0174	0.0494	-0.0013	-0.0001	0.0397	0.0081	0.0396	27.9791	-1.6206	24.0285
6	11.0821	1.5675	-5.5984	0.2988	-1.1595	4.5813	-0.2738	0.2381	-0.4013	-0.1508	0.1297	-0.181	0.4579	0.0819	0.1442	0.0555	-0.0178	0.0316	0.0278	-0.0642	0.0202	38.4471	-4.457	2.0132
7	8.7673	3.746	-7.2497	1.7212	-3.5303	7.5461	-0.5403	0.2825	-0.5866	-0.3055	0.2212	-0.2717	0.8436	-0.2914	0.3191	0.0773	-0.0658	0.0354	0.0142	-0.093	0.0285	30.6375	-8.6454	4.2754
8	1.9469	0.0803	-0.2254	2.9302	0.5895	2.5215	-0.0063	0.0302	0.0567	-0.0394	0.0605	-0.0301	-0.0287	-0.1923	-0.0542	0.0472	0.001	-0.0047	0.0381	0.0153	0.0414	29.0377	2.6315	18.8657
9	9.2118	-0.1451	-3.8616	10.5689	8.077	11.3515	-0.1368	0.1741	-0.889	0.5707	0.2847	-0.4421	1.2399	0.5839	-0.1479	0.0776	0.0778	-0.0305	0.0108	-0.0775	0.0676	19.0932	-11.2401	31.9007
10	6.0909	0.7311	1.7081	1.7117	0.1042	5.3292	-0.1758	0.4025	-0.0544	-0.0224	0.2757	0.0226	-0.0745	0.103	-0.0999	0.0146	-0.0302	0.0166	0.0628	-0.0015	0.0162	14.2706	-2.5286	29.5727
11	5.637	6.298	-0.6855	14.4224	-0.3584	0.1058	-0.8955	1.6635	2.5075	-1.9048	0.0276	-0.1427	-0.6074	0.7948	0.8678	0.2336	-0.0537	-0.0662	0.1067	0.1436	0.0035	11.3583	10.4669	22.6442
12	3.7882	-3.7634	0.6187	16.9594	2.1642	0.6852	-0.3624	0.9614	0.2425	-1.0734	0.1982	-0.121	-0.3508	0.2992	0.1642	0.1167	-0.1497	-0.0549	0.1956	0.087	-0.1067	8.2185	1.9464	18.3808
13	14.8036	7.0092	7.7555	13.3612	6.1341	4.6666	0.0365	0.3612	-1.1003	-0.5279	-0.0024	-0.1615	0.115	0.1798	-0.0342	0.0209	-0.071	0.0458	0.1206	-0.0686	-0.0062	9.4905	-8.0511	20.3843
14	1.6296	0.4162	1.0477	1.097	1.2379	1.6241	-0.1326	0.1737	0.0808	-0.1762	0.0772	0.0345	-0.1339	0.0543	0.0554	0.0409	-0.0244	-0.0043	0.0177	0.0067	0.059	12.4687	2.5168	33.2096
15	6.6522	5.7209	0.8999	9.2285	1.7999	0.3661	-0.1678	-0.2329	-0.1945	0.0449	0.0362	0.2118	0.0966	-0.0934	0.1316	0.0332	-0.0028	0.0216	0.038	0.0282	0.0753	6.8807	-3.1217	46.7845
16	0.6835	0.5556	-0.0146	0.972	0.6337	0.8802	-0.1178	0.0074	0.0992	-0.1399	0.0105	0.1507	-0.0914	-0.068	0.1073	0.042	-0.0025	-0.0327	0.0038	0.0067	0.0721	9.2015	5.6985	39.5634
17	1.7822	-0.3776	2.3721	3.7954	3.0433	6.5411	-0.0641	0.5246	-0.2679	-0.4224	-0.1344	0.2675	-0.2267	0.0352	0.1985	0.0267	-0.03	-0.0178	0.0701	-0.0592	0.0039	-1.3399	-4.8203	17.6775
18	0.4318	0.825	1.2012	1.7849	1.9927	5.1649	-0.2926	0.0837	0.2386	-0.3652	-0.0091	0.3159	-0.552	-0.2046	0.3017	0.0659	-0.0085	-0.096	-0.0106	0.0237	0.0605	3.6034	7.24	29.3106
19	5.4393	-1.487	1.116	2.2246	-0.514	2.6347	-0.0421	0.0516	-0.1236	-0.0665	0.0119	0.1164	0.0773	0.0111	0.0302	0.057	-0.0166	0.0066	0.0121	-0.0013	0.0646	12.7731	-2.9149	40.2902

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 6	1 - 6
2	X-RAY DIFFRACTION	2	A	A	7 - 16	7 - 16
3	X-RAY DIFFRACTION	3	A	A	17 - 23	17 - 23
4	X-RAY DIFFRACTION	4	A	A	24 - 57	24 - 57
5	X-RAY DIFFRACTION	5	A	A	58 - 77	58 - 77
6	X-RAY DIFFRACTION	6	A	A	78 - 96	78 - 96
7	X-RAY DIFFRACTION	7	A	A	97 - 104	97 - 104
8	X-RAY DIFFRACTION	8	A	A	105 - 124	105 - 124
9	X-RAY DIFFRACTION	9	B	B	1 - 6	1 - 6
10	X-RAY DIFFRACTION	10	B	B	7 - 14	7 - 14
11	X-RAY DIFFRACTION	11	B	B	15 - 23	15 - 23
12	X-RAY DIFFRACTION	12	B	B	24 - 31	24 - 31
13	X-RAY DIFFRACTION	13	B	B	32 - 39	32 - 39
14	X-RAY DIFFRACTION	14	B	B	40 - 59	40 - 59
15	X-RAY DIFFRACTION	15	B	B	60 - 70	60 - 70
16	X-RAY DIFFRACTION	16	B	B	71 - 83	71 - 83
17	X-RAY DIFFRACTION	17	B	B	84 - 96	84 - 96
18	X-RAY DIFFRACTION	18	B	B	97 - 106	97 - 106
19	X-RAY DIFFRACTION	19	B	B	107 - 124	107 - 124

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