PDB-6c5a: Human UDP-Glucose Dehydrogenase with UDP- Glc and NADH bound

ID or keywords:

Entry

Database: PDB / ID: 6c5a

Title

Human UDP-Glucose Dehydrogenase with UDP- Glc and NADH bound

Components

UDP-glucose 6-dehydrogenase

Keywords

OXIDOREDUCTASE / dehydrogenase / udp-glucose / hUGDH / hexamer

Function / homology

Function and homology information

Formation of the active cofactor, UDP-glucuronate / chondroitin sulfate biosynthetic process / UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / gastrulation with mouth forming second / protein hexamerization / neuron development ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Gross, P.G. / Fallah, J. / Wood, Z.A.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: The A225L Substitution of hUGDH alters structure and function
Authors: Gross, P.G. / Wood, Z.A.

History

Deposition	Jan 15, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 16, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6c5a.cif.gz	1.1 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	6c5a_validation.pdf.gz	4.2 MB	Display	wwPDB validaton report
Full document	6c5a_full_validation.pdf.gz	4.3 MB	Display
Data in XML	6c5a_validation.xml.gz	102.6 KB	Display
Data in CIF	6c5a_validation.cif.gz	140.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c5/6c5a ftp://data.pdbj.org/pub/pdb/validation_reports/c5/6c5a	HTTPS FTP

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Related structure data

Related structure data	6c58C 6c5zC C: citing same article (ref.)
Similar structure data	2q3e-2 2qg4-6 2qg4-5 2qg4-4 6c4j-2 2q3e-1 3khu-d 2qg4-1 4rjt-1 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	#254 - Feb 2021 Cellulose Synthase similarity (1) #111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1) #102 - Jun 2008 Lactate Dehydrogenase similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #127 - Jul 2010 Crystallins similarity (1)

Deposited unit

A: UDP-glucose 6-dehydrogenase

B: UDP-glucose 6-dehydrogenase

C: UDP-glucose 6-dehydrogenase

D: UDP-glucose 6-dehydrogenase

E: UDP-glucose 6-dehydrogenase

F: UDP-glucose 6-dehydrogenase

hetero molecules

338 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: Assembly is supported by sedimentation velocity using analytical ultracentrifugation.

Unit cell

Length a, b, c (Å)	95.450, 199.870, 200.520
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	UDP-glucose 6-dehydrogenase / UDPGDH Mass: 55093.938 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UGDH / Production host: Escherichia coli (E. coli) / References: UniProt: O60701, UDP-glucose 6-dehydrogenase
#2: Chemical	ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH Mass: 665.441 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₁H₂₉N₇O₁₄P₂
#3: Chemical	ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER Mass: 566.302 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₅H₂₄N₂O₁₇P₂
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 656 / 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: 2.89 Å³/Da / Density % sol: 57.49 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 13% PEG3350; 50 mM dipotassium phosphate, 100 mM Tris

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Data collection

Diffraction	Mean temperature: 77 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 20, 2017
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→56.854 Å / Num. obs: 170376 / % possible obs: 99.9 % / Redundancy: 7.43 % / CC_1/2: 0.998 / R_rim(I) all: 0.116 / R_sym value: 0.108 / Net I/σ(I): 12.18
Reflection shell	Resolution: 2.3→2.35 Å / Redundancy: 7.59 % / Mean I/σ(I) obs: 1.33 / Num. unique obs: 12480 / CC_1/2: 0.647 / R_rim(I) all: 1.844 / R_sym value: 1.718 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
Coot	0.8.2	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→54.751 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.07

	R_factor	Num. reflection	% reflection
R_free	0.2211	8510	5 %
R_work	0.1925	-	-
obs	0.1939	170192	99.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.3→54.751 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21568	0	496	656	22720

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	22484
X-RAY DIFFRACTION	f_angle_d	1.034	30496
X-RAY DIFFRACTION	f_dihedral_angle_d	19.162	8366
X-RAY DIFFRACTION	f_chiral_restr	0.072	3483
X-RAY DIFFRACTION	f_plane_restr	0.006	3853

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 (%)
2.3-2.3261	0.3732	284	0.3491	5357	X-RAY DIFFRACTION	100
2.3261-2.3535	0.3725	273	0.3304	5331	X-RAY DIFFRACTION	100
2.3535-2.3822	0.3762	285	0.3217	5357	X-RAY DIFFRACTION	100
2.3822-2.4124	0.3404	276	0.3062	5317	X-RAY DIFFRACTION	100
2.4124-2.4441	0.3328	288	0.2922	5348	X-RAY DIFFRACTION	100
2.4441-2.4776	0.3284	279	0.2818	5313	X-RAY DIFFRACTION	100
2.4776-2.513	0.2882	273	0.2705	5386	X-RAY DIFFRACTION	100
2.513-2.5505	0.2831	289	0.2624	5297	X-RAY DIFFRACTION	100
2.5505-2.5903	0.2834	281	0.2681	5347	X-RAY DIFFRACTION	100
2.5903-2.6328	0.3248	282	0.2578	5359	X-RAY DIFFRACTION	100
2.6328-2.6782	0.2717	277	0.2598	5335	X-RAY DIFFRACTION	100
2.6782-2.7269	0.268	285	0.242	5367	X-RAY DIFFRACTION	100
2.7269-2.7794	0.2664	278	0.2309	5346	X-RAY DIFFRACTION	100
2.7794-2.8361	0.2854	283	0.2326	5355	X-RAY DIFFRACTION	100
2.8361-2.8977	0.2677	280	0.2309	5393	X-RAY DIFFRACTION	100
2.8977-2.9652	0.2783	285	0.2345	5326	X-RAY DIFFRACTION	100
2.9652-3.0393	0.3247	286	0.2329	5388	X-RAY DIFFRACTION	100
3.0393-3.1215	0.2365	279	0.2289	5385	X-RAY DIFFRACTION	100
3.1215-3.2133	0.2776	284	0.2202	5376	X-RAY DIFFRACTION	100
3.2133-3.317	0.2644	287	0.2193	5385	X-RAY DIFFRACTION	100
3.317-3.4355	0.2496	281	0.2213	5366	X-RAY DIFFRACTION	100
3.4355-3.5731	0.2504	283	0.2119	5404	X-RAY DIFFRACTION	100
3.5731-3.7357	0.2077	278	0.1889	5367	X-RAY DIFFRACTION	100
3.7357-3.9326	0.2022	285	0.1798	5402	X-RAY DIFFRACTION	99
3.9326-4.1789	0.1829	288	0.1629	5422	X-RAY DIFFRACTION	100
4.1789-4.5014	0.1564	285	0.1428	5415	X-RAY DIFFRACTION	100
4.5014-4.9541	0.173	290	0.1327	5462	X-RAY DIFFRACTION	100
4.9541-5.6703	0.18	295	0.1513	5499	X-RAY DIFFRACTION	100
5.6703-7.1415	0.1893	288	0.1611	5541	X-RAY DIFFRACTION	100
7.1415-54.7662	0.1511	303	0.1398	5736	X-RAY DIFFRACTION	99

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	0.687	0.1803	-0.2399	0.8381	-0.1247	0.7775	0.1657	0.1913	0.2491	-0.8559	0.3099	-0.9052	-0.2064	0.9673	0.7897	0.8411	-0.4175	1.0828	1.0108	-0.5454	0.6681	149.2895	70.282	399.8536
2	1.196	0.2168	-0.0148	1.6503	0.059	1.1873	0.1525	-0.2115	0.4197	-0.205	0.2827	-0.5014	-0.6113	0.6472	-0.4043	0.8271	-0.2896	0.3788	0.7969	-0.3547	0.8225	141.431	76.4006	413.4895
3	1.0768	-0.5404	-1.0083	1.6914	-0.342	1.4982	0.228	0.05	0.4724	-0.6161	0.2166	-0.4292	-0.7207	0.3481	-0.2471	0.9062	-0.22	0.3052	0.4484	-0.0827	0.4949	127.811	75.74	405.7657
4	1.7093	-0.946	0.2171	2.1857	-0.2165	1.7001	0.1369	0.2443	0.1016	-0.8588	-0.0913	-0.0032	-0.1443	-0.0724	-0.0727	0.7095	-0.0368	0.0226	0.4593	-0.0192	0.37	114.459	61.3455	401.9251
5	0.4222	-0.7583	-0.2603	3.2314	1.0519	1.1672	-0.0893	-0.2277	0.0148	0.0606	0.1523	-0.1064	0.0963	0.1982	-0.0677	0.5034	-0.0096	0.0553	0.4549	-0.0034	0.3168	121.1843	60.6842	418.781
6	1.4078	1.0907	-0.2892	3.4522	-0.0511	1.0626	-0.2003	0.0338	-0.2061	-0.3506	0.1447	-0.2864	0.2536	0.1182	0.105	0.6492	-0.0007	0.1457	0.4349	-0.0466	0.4203	129.8698	44.006	409.1012
7	3.5893	1.6322	0.3176	3.8053	-0.3859	0.7272	-0.1816	0.1558	-0.465	-0.3859	0.1702	-0.7895	0.4403	0.4505	-0.0283	0.6121	0.0402	0.1936	0.483	-0.0494	0.5097	135.1378	39.3811	407.753
8	1.9654	1.2347	-1.2739	3.7381	0.4637	2.1804	-0.2839	0.331	-0.1382	-1.1651	0.1991	-0.075	0.2276	-0.1234	0.0677	0.8711	-0.112	0.1307	0.5404	-0.0577	0.3925	123.877	38.5351	397.4152
9	1.1958	0.1359	-0.2461	5.7352	1.1742	1.223	-0.167	0.4367	0.0788	-1.4218	-0.08	0.656	0.268	-0.6781	0.1655	0.9497	-0.1293	-0.0058	0.5643	-0.0633	0.4999	114.6844	42.3111	398.4074
10	1.9527	0.2562	-0.0565	2.8075	0.7458	2.8518	0.1669	0.2428	0.0483	-0.7629	-0.2303	0.6613	-0.1819	-0.626	0.0855	0.9143	0.2181	-0.3936	0.7782	-0.0519	0.8634	82.2305	74.5573	396.0592
11	1.7579	0.3882	0.108	2.065	0.1254	2.1812	0.1487	0.2823	-0.2609	-0.5234	-0.0633	0.7562	0.1073	-0.2673	-0.0926	0.7514	0.1027	-0.2842	0.517	-0.0809	0.7496	88.3007	60.8092	403.8824
12	0.8677	-0.8316	-0.272	1.7666	0.5261	1.4866	0.1074	0.1643	-0.0569	-0.4996	-0.0636	0.2355	-0.1195	-0.1674	-0.05	0.54	0.0019	-0.052	0.3899	-0.0144	0.2728	107.0148	69.3541	409.2353
13	1.8568	0.1644	0.4245	3.0194	1.1575	2.5545	-0.0318	0.1598	0.2642	-0.4329	0.0888	0.1434	-0.5409	-0.0358	-0.045	0.6174	0.0478	0.0082	0.3747	0.037	0.3585	102.0245	92.9931	420.8183
14	2.4654	0.328	0.4238	3.0116	0.2871	2.2518	-0.1154	0.0931	-0.5669	0.1938	0.1598	-0.4522	0.6228	0.216	-0.0522	0.9506	0.063	0.1363	0.3754	-0.0181	0.5752	117.471	6.4263	426.4352
15	1.1437	0.6686	-0.414	1.8553	0.1967	1.1024	-0.0485	0.0489	-0.0676	0.0189	-0.0209	0.0056	0.2822	-0.08	0.0645	0.8414	-0.0029	0.1156	0.3812	0.0157	0.3723	107.048	22.5004	428.3782
16	2.1906	0.1749	1.2608	1.7967	0.5448	1.9948	0.0909	-0.2172	-0.1566	0.7565	0.0393	-0.39	0.4711	0.0349	-0.1209	1.1015	0.0168	-0.0121	0.4125	0.0239	0.4565	121.3392	29.7355	451.7607
17	2.619	1.1763	0.0859	4.2155	1.2081	2.5431	-0.3106	-0.1588	0.3176	-0.4097	-0.4804	1.6105	-0.6443	-0.7241	0.6549	0.8912	0.18	-0.0052	0.5445	-0.1538	0.9807	70.9013	37.6905	463.7862
18	1.5103	0.7299	0.0327	2.2198	0.7068	1.1065	-0.2489	-0.1249	0.0395	-0.3611	0.0543	0.2748	-0.4423	0.1365	0.1747	1.0034	0.0485	0.1555	0.426	0.0479	0.4533	86.6538	40.8137	465.6185
19	0.6689	-0.054	0.2154	1.6308	-0.4486	1.5945	-0.0152	-0.0027	0.1155	0.2693	-0.0322	0.6402	-0.0111	-0.1097	0.019	0.7161	-0.0482	0.2246	0.3747	-0.0388	0.5805	89.8542	41.7258	438.3721
20	1.5261	-0.6007	-0.0692	2.4423	0.2496	3.0717	-0.1804	0.2235	-0.1923	-0.023	-0.1535	1.5366	0.4057	-0.7636	0.2995	0.6023	-0.1251	0.065	0.6047	-0.1541	1.2121	75.4103	43.3918	424.3558
21	3.0864	0.3758	0.5505	3.9516	0.6486	1.9281	-0.0757	-0.5363	0.1788	0.073	0.2228	-2.6973	-0.0142	0.1965	-0.1474	0.7643	0.1259	-0.1193	0.5834	-0.0654	1.6328	149.236	55.0308	477.4649
22	1.9014	0.6165	0.5255	3.9586	0.6888	1.2597	0.0122	-0.2208	-0.1982	-0.5507	-0.0102	-0.663	0.0968	-0.1597	-0.0415	0.8371	0.1779	-0.0386	0.5662	-0.0188	0.4765	133.5332	52.5336	473.7361
23	0.7625	0.424	0.1031	0.8401	0.7621	2.2462	-0.0493	0.099	-0.2445	0.2947	0.5189	-0.5718	0.4791	0.9364	-0.385	0.7584	0.2632	-0.1489	0.7901	-0.2741	0.625	137.7422	68.9732	449.9137
24	0.8559	0.5702	-0.3982	0.7814	-0.8703	1.0902	0.0804	-0.2014	0.356	0.3939	0.8093	-1.2828	-0.6393	1.3577	-0.2717	0.8919	-0.1765	-0.0185	1.3654	-0.7272	1.1763	148.7983	84.2297	441.1673
25	1.843	0.7207	-0.7299	2.4445	0.0352	2.4159	0.1562	-0.0967	0.227	0.4229	0.0399	0.141	-0.4681	0.0538	-0.2185	0.7482	0.0957	0.0852	0.3724	-0.0424	0.4336	106.4057	105.2266	461.203
26	1.2822	1.2241	0.013	3.8384	0.4979	1.1264	0.075	0.0449	0.0449	-0.1163	0.0967	-0.0613	-0.1323	0.0417	-0.1658	0.5744	0.0683	0.0573	0.3863	-0.0147	0.3841	109.319	95.8936	444.5413
27	1.1619	-0.1507	0.1997	2.368	-0.7162	1.6436	0.0174	0.0148	0.0154	0.0785	-0.0018	-0.2439	-0.0921	0.243	-0.0338	0.6053	-0.011	0.0597	0.3578	-0.0815	0.4404	118.2988	99.9718	450.7599
28	1.9495	-0.2312	-1.3543	1.6768	1.3428	4.7779	0.0883	0.0139	0.2627	0.1802	0.0853	-0.6387	-0.7078	0.5719	-0.1843	0.766	-0.0485	-0.0037	0.4642	-0.1139	0.6283	126.3429	103.6084	457.2777
29	1.6537	0.2828	-0.625	0.9837	0.1445	1.2199	0.0334	0.0297	-0.0815	0.2375	0.0712	-0.0974	0.2831	-0.0031	-0.0924	0.7448	0.1001	-0.0732	0.3439	-0.0278	0.3605	111.3128	73.1175	458.9837
30	4.2162	2.7801	0.2499	8.804	1.1933	2.7716	0.0966	-0.1312	0.536	0.1672	-0.0596	0.8327	0.2186	-0.5151	-0.0798	0.7161	0.0905	0.0584	0.4017	0.0241	0.4753	91.4381	79.2474	463.7424
31	2.1047	0.6354	-0.4075	2.7555	0.5079	1.8009	0.0287	-0.5006	0.0989	0.9034	-0.0393	0.0834	0.112	0.0362	0.021	1.1441	0.0376	0.0251	0.4876	-0.0135	0.4199	97.9789	68.3332	475.3894

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 87 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 88 through 185 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 186 through 244 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 245 through 276 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 277 through 321 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 322 through 372 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 373 through 413 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 414 through 440 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 441 through 465 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 87 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 88 through 185 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 186 through 321 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 322 through 465 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1 through 87 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 88 through 276 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 277 through 465 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1 through 87 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 88 through 204 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 205 through 372 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 373 through 465 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 2 through 87 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 88 through 204 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 205 through 417 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 418 through 465 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 2 through 87 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 88 through 135 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 136 through 185 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 186 through 212 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 213 through 360 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 361 through 389 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 390 through 466 )

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