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- PDB-5pzy: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosph... -

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Open data

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Basic information

Entry

Database: PDB / ID: 5pzy

Title

Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-(5-bromo-1,3-thiazol-2-yl)-3-(2-chlorophenyl)sulfonylurea

Components

Fructose-1,6-bisphosphatase 1

Fructose 1,6-bisphosphatase

Keywords

HYDROLASE/HYDROLASE INHIBITOR / D3R docking / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

Fructose-1,6-bisphosphatase class 1 /

Fructose-1,6-bisphosphatase, active site /

Fructose-1,6-bisphosphatase / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase active site. / fructose 1,6-bisphosphate 1-phosphatase activity / carbohydrate metabolic process /

Fructose-1,6-bisphosphatase 1

Function and homology information

Specimen source

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / 2.21 Å resolution

Model details

For D3R project

Authors

Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G. / Yang, H. / Shao, C. / Burley, S.K.

Citation

Journal: To be published
Title: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-(5-bromo-1,3-thiazol-2-yl)-3-(2-chlorophenyl)sulfonylurea
Authors: Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G.

Validation Report

Summary

Full report

About validation report

Date

Deposition: Apr 18, 2017 / Release: Jan 9, 2019

Revision	Date	Data content type	Group	Category	Item	Provider	Type
1.0	Jan 9, 2019	Structure model				repository	Initial release
1.1	Jan 16, 2019	Structure model	Data collection	diffrn_radiation	_diffrn_radiation.pdbx_diffrn_protocol
1.2	Feb 6, 2019	Structure model	Data collection / Database references / Structure summary	audit_author / citation_author	_audit_author.name / _citation_author.name

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmcif format	5pzy.cif.gz / Display in browser / Tree view / PDBx/mmCIF dictionary
PDB format	pdb5pzy.ent.gz / Display in browser / PDB Contents Guide
PDBML Plus	5pzy-add.xml.gz / Display in browser*PLUS
Others	Other downloads

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Links

PDB pages	PDBj / RCSB PDB / PDBe / NCBI

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Related structure data

Similar-shape strucutres	Search similar-shape structures by Omokage search Omokage search

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Assembly

Deposited unit

A: Fructose-1,6-bisphosphatase 1

B: Fructose-1,6-bisphosphatase 1

C: Fructose-1,6-bisphosphatase 1

D: Fructose-1,6-bisphosphatase 1

E: Fructose-1,6-bisphosphatase 1

F: Fructose-1,6-bisphosphatase 1

G: Fructose-1,6-bisphosphatase 1

H: Fructose-1,6-bisphosphatase 1

hetero molecules

298 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

A: Fructose-1,6-bisphosphatase 1

B: Fructose-1,6-bisphosphatase 1

C: Fructose-1,6-bisphosphatase 1

D: Fructose-1,6-bisphosphatase 1

hetero molecules

defined by author&software
149 kDa, 4 polymers
Download structure data
Search similar-shape structures of this assembly by Omokage search (details)

E: Fructose-1,6-bisphosphatase 1

F: Fructose-1,6-bisphosphatase 1

G: Fructose-1,6-bisphosphatase 1

H: Fructose-1,6-bisphosphatase 1

hetero molecules

defined by author&software
149 kDa, 4 polymers
Download structure data
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.214, 283.778, 83.368
Angle α, β, γ (deg.)	90.000, 97.310, 90.000
Int Tables number	4
Space group name H-M	P 1 21 1

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Components

#1: Protein/peptide	Fructose-1,6-bisphosphatase 1 / Fructose 1,6-bisphosphatase / Growth-inhibiting protein 17 / cDNA FLJ75786 / highly similar to Homo sapiens fructose-1 / 6-bisphosphatase 1 (FBP1) / mRNA Mass: 36859.418 Da / Num. of mol.: 8 / Source: (gene. exp.) Homo sapiens (human) / Gene: FBP1, hCG_1640493 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2TU34, fructose-bisphosphatase
#2: Chemical	ChemComp-94V / N-[(5-bromo-1,3-thiazol-2-yl)carbamoyl]-2-chlorobenzene-1-sulfonamide Mass: 396.668 Da / Num. of mol.: 8 / Formula: C₁₀H₇BrClN₃O₃S₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 927 / Formula: H₂O / Water

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.72 / Density percent sol: 54.8 %
Crystal grow	Temp: 300 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M HEPES pH 7.0, 0.1M AMMONIUM ACETATE, 12%-25% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 kelvins
Source	Source: SYNCHROTRON / Type: SLS BEAMLINE X10SA / Synchrotron site: SLS / Beamline: X10SA / Wavelength: 0.987
Detector	Type: MAR CCD 165 mm / Detector: CCD / Collection date: Oct 20, 2005
Radiation	Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	D resolution high: 2.21 Å / D resolution low: 24.255 Å / Number obs: 140872 / Percent possible obs: 93.01

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Language: C++ / Type: package

Name	Version	Classification	Contact author	Contact author email	Location	Date
PHENIX	1.11.1_2575	refinement	Paul D. Adams	PDAdams[at]lbl.gov	http://www.phenix-online.org/
PDB_EXTRACT	3.23	data extraction	PDB	deposit[at]deposit.rcsb.org	http://sw-tools.pdb.org/apps/PDB_EXTRACT/	Dec. 13, 2016

Refine

Method to determine structure:

MOLECULAR REPLACEMENT / Overall SU ML: 0.29 / Cross valid method: THROUGHOUT / Sigma F: 1.36 / Overall phase error: 23.81 / Stereochemistry target values: ML

Solvent computation

Solvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL

Displacement parameters

B iso max: 137.25 Å² / B iso mean: 42.422 Å² / B iso min: 9.2 Å²

Least-squares process

R factor R free: 0.228 / R factor R work: 0.1726 / R factor obs: 0.1754 / Highest resolution: 2.21 Å / Lowest resolution: 24.255 Å / Number reflection R free: 7106 / Number reflection R work: 133766 / Number reflection obs: 140872 / Percent reflection R free: 5.04 / Percent reflection obs: 93.01

Refine hist #final

Highest resolution: 2.21 Å / Lowest resolution: 24.255 Å / B iso mean ligand: 47.55 / B iso mean solvent: 42.62 / Number residues total: 2540

Number of atoms included #final

Protein: 19440 / Nucleic acid: 0 / Ligand: 160 / Solvent: 927 / Total: 20527

Refine LS restraints

Refine ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	19985
X-RAY DIFFRACTION	f_angle_d	0.964	27001
X-RAY DIFFRACTION	f_chiral_restr	0.058	3054
X-RAY DIFFRACTION	f_plane_restr	0.006	3450
X-RAY DIFFRACTION	f_dihedral_angle_d	10.296	12137

Refine LS restraints ncs

Ens ID: 1 / Number: 12223 / Refine ID: X-RAY DIFFRACTION / Rms: 9.324 / Type: TORSIONAL

Dom ID	Auth asym ID
1	A
2	B
3	C
4	D
5	E
6	F
7	G
8	H

Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 30

Highest resolution	R factor R free	R factor R work	Lowest resolution	Number reflection R free	Number reflection R work	Number reflection all	Percent reflection obs
2.2100	0.3082	0.2706	2.2351	207	3786	3993	80.0000
2.2351	0.3325	0.2626	2.2614	222	3885	4107	81.0000
2.2614	0.2988	0.2439	2.2889	216	3928	4144	83.0000
2.2889	0.3230	0.2355	2.3179	249	4082	4331	86.0000
2.3179	0.2797	0.2222	2.3484	212	4077	4289	85.0000
2.3484	0.2696	0.2231	2.3805	214	4195	4409	87.0000
2.3805	0.3072	0.2267	2.4145	217	4190	4407	89.0000
2.4145	0.3090	0.2356	2.4505	237	4387	4624	90.0000
2.4505	0.3086	0.2338	2.4887	235	4354	4589	93.0000
2.4887	0.2924	0.2149	2.5295	241	4497	4738	93.0000
2.5295	0.2763	0.2247	2.5731	266	4557	4823	96.0000
2.5731	0.3006	0.2200	2.6198	233	4671	4904	97.0000
2.6198	0.2667	0.2060	2.6701	240	4679	4919	97.0000
2.6701	0.2539	0.1897	2.7246	235	4679	4914	98.0000
2.7246	0.2718	0.1839	2.7837	230	4750	4980	98.0000
2.7837	0.2247	0.1789	2.8484	255	4657	4912	98.0000
2.8484	0.2473	0.1790	2.9195	270	4643	4913	98.0000
2.9195	0.2657	0.1822	2.9983	257	4751	5008	98.0000
2.9983	0.2350	0.1781	3.0864	233	4665	4898	98.0000
3.0864	0.2346	0.1753	3.1858	239	4728	4967	98.0000
3.1858	0.2345	0.1756	3.2994	212	4719	4931	97.0000
3.2994	0.2375	0.1673	3.4311	251	4628	4879	97.0000
3.4311	0.2287	0.1623	3.5868	227	4648	4875	97.0000
3.5868	0.2071	0.1569	3.7752	273	4607	4880	96.0000
3.7752	0.2102	0.1482	4.0108	257	4592	4849	96.0000
4.0108	0.1749	0.1413	4.3189	233	4595	4828	95.0000
4.3189	0.1658	0.1271	4.7505	255	4604	4859	95.0000
4.7505	0.1755	0.1341	5.4312	216	4557	4773	95.0000
5.4312	0.2025	0.1628	6.8175	245	4584	4829	95.0000
6.8175	0.1845	0.1461	24.2561	229	4071	4300	84.0000

Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

ID	L11	L12	L13	L22	L23	L33	S11	S12	S13	S21	S22	S23	S31	S32	S33	T11	T12	T13	T22	T23	T33	Origin x	Origin y	Origin z
1	0.3245	0.2845	-0.1037	0.5850	-0.2782	0.1762	-0.1180	-0.0252	0.0814	-0.1265	-0.0167	-0.0310	-0.1142	0.1083	-0.0167	0.1855	-0.0073	0.0322	0.1469	0.0141	0.1633	37.4011	16.0105	-5.5187
2	0.5197	-0.4312	-0.1479	0.2189	-0.0337	0.2667	-0.0272	-0.0357	0.0541	-0.2060	0.0057	0.1475	-0.0118	0.0753	0.0004	0.2453	0.0012	-0.0652	0.1438	0.0178	0.2397	19.8192	22.8417	-7.8225
3	0.2529	-0.1527	0.0270	0.1102	-0.1178	0.1365	-0.0129	-0.0257	0.1328	-0.0791	0.0367	0.0923	-0.2055	-0.0176	0.0326	0.3962	0.0171	-0.1037	0.1421	0.0096	0.3128	18.1126	31.3045	-10.2229
4	0.6802	-0.4599	-0.2892	0.8709	-0.1868	0.3873	-0.0612	-0.1417	-0.1948	-0.1724	0.0219	0.1774	0.1745	0.0661	-0.0261	0.0932	-0.0020	0.0245	0.2236	0.0341	0.2900	12.6091	-2.9126	15.9504
5	0.5066	-0.1304	-0.0469	0.3805	0.0152	0.3661	-0.0951	-0.1180	0.0074	-0.0242	0.0149	0.1606	-0.1126	0.0187	-0.0579	0.0735	0.0416	0.0086	0.1757	-0.0262	0.2467	9.0224	15.5577	16.2264
6	0.3678	-0.0910	0.0095	0.3331	-0.2371	1.0504	0.0227	-0.0847	-0.1059	0.0385	-0.0104	0.1842	-0.9538	0.0483	-0.0077	-0.1957	0.1730	0.0135	0.2075	-0.0500	0.4441	0.9318	18.9692	17.7307
7	0.2800	-0.3096	-0.3795	0.4031	0.3520	0.4346	-0.0427	0.0329	-0.0077	-0.1974	0.0102	0.1022	0.0347	0.0167	-0.0066	0.1882	0.0399	0.0083	0.1877	0.0212	0.1290	35.9855	-8.9807	-11.3961
8	0.2036	-0.1356	0.0071	0.2899	-0.0796	0.4898	0.0050	0.0443	-0.0098	-0.1949	-0.0501	-0.0083	0.1104	0.0920	-0.0331	0.1744	0.0468	0.0735	0.2136	0.0228	0.1665	53.6860	-18.7239	-7.1320
9	0.0347	-0.1577	0.1690	0.1195	-0.2010	0.4662	0.0173	-0.0969	0.0478	0.0533	0.0152	0.0058	-0.0326	-0.0247	0.0061	0.0762	-0.0023	0.0439	0.2278	0.0180	0.1849	32.8206	-4.6534	21.1679
10	0.0576	-0.0664	0.0592	0.0464	0.0076	0.0615	0.1494	0.2085	-0.1720	0.1837	-0.0968	0.0348	-0.1673	0.1541	-0.0001	0.2946	0.0411	0.0008	0.2876	-0.0094	0.2261	43.8048	-4.2318	33.8832
11	0.2034	-0.0685	0.0467	0.3476	-0.2867	0.1612	0.0002	0.0070	0.0677	0.1619	-0.0027	-0.1604	-0.0583	0.0534	0.0009	0.2028	0.0231	0.0111	0.2273	0.0305	0.1435	41.6724	-10.0442	30.9552
12	0.1590	-0.0759	0.0067	0.3340	-0.3693	0.4161	0.0107	-0.0411	-0.0215	-0.0052	-0.0071	0.0339	0.1481	0.0237	-0.0375	0.1345	0.0295	-0.0016	0.1329	0.0206	0.1336	41.5965	-25.6072	15.8425
13	0.1035	-0.1755	-0.2300	0.0187	0.0826	0.1846	-0.0085	-0.0430	0.0369	0.0687	0.0271	-0.0216	0.0730	0.0577	0.0034	0.2274	0.0650	-0.0174	0.1695	0.0368	0.1377	47.5975	-26.8982	24.7232
14	0.3662	-0.0552	0.0778	0.4612	-0.2701	0.3633	0.0702	-0.0617	-0.1586	0.1080	-0.0659	-0.0324	0.0271	0.2044	0.0001	0.2975	-0.0134	-0.0213	0.2266	0.0065	0.2931	-0.6090	51.0459	42.6566
15	0.4703	-0.1395	-0.1677	0.2966	0.1916	0.2650	0.0489	-0.0479	-0.3315	0.0752	0.0387	0.2058	0.1016	-0.0709	-0.0119	0.2701	-0.0401	-0.0349	0.1410	0.0719	0.2903	-5.9004	43.1845	46.1698
16	0.0122	-0.0019	0.1949	0.0448	-0.1007	0.3260	0.0403	-0.1629	-0.3411	0.1328	0.0462	-0.0517	-0.1793	-0.2803	0.0073	0.1784	-0.0776	0.0320	0.3122	-0.0161	0.4624	-26.4579	43.8905	37.7407
17	0.0888	0.0087	0.1772	0.1520	-0.2361	0.1306	0.1288	-0.0410	-0.2306	0.1796	-0.1224	0.0728	0.2954	-0.1397	-0.0017	0.3522	-0.0893	0.0166	0.2231	0.0216	0.4496	-20.6860	35.2259	43.1089
18	0.6649	0.1437	0.1372	0.2552	-0.1262	0.2400	-0.0872	0.1811	0.0566	-0.0338	-0.0017	0.1445	-0.2545	-0.0383	-0.0017	0.2805	0.0169	-0.0656	0.2606	-0.0149	0.2292	-18.5120	69.4467	16.3862
19	0.8771	0.0301	0.0263	0.3318	0.0908	0.0947	0.0514	0.2556	-0.3000	-0.0744	-0.1600	0.1382	-0.1186	-0.0588	-0.0590	0.1685	-0.0186	-0.0669	0.3288	-0.1526	0.3121	-22.4066	50.9809	15.2711
20	0.1697	0.1208	-0.0441	0.1780	-0.1305	0.1156	0.0276	0.2834	-0.2369	0.0289	0.0507	0.1106	-0.0725	-0.0140	0.0123	0.2176	0.0092	-0.0720	0.3437	-0.1639	0.3784	-30.0799	47.8806	11.8889
21	0.2141	-0.1074	0.2444	0.5599	0.4404	0.3372	0.0251	-0.0441	0.0495	0.0776	-0.0336	-0.0093	-0.0330	-0.0515	0.0001	0.2886	-0.0702	0.0105	0.1921	0.0173	0.1592	-2.7967	74.8698	48.9889
22	0.3190	0.2440	-0.1530	0.4940	-0.2412	0.4727	0.0662	-0.0703	0.0183	0.1637	-0.0625	-0.0689	-0.0157	0.0587	0.0001	0.2372	-0.0674	-0.0277	0.1917	0.0015	0.1391	15.5564	84.2829	49.5355
23	0.0312	-0.0311	0.0146	0.0304	-0.0371	0.0321	-0.0985	0.1982	0.0522	-0.0357	-0.0448	0.1355	-0.0654	-0.0892	-0.0003	0.3196	-0.0059	-0.0734	0.4929	0.0564	0.2209	-8.9089	79.6389	8.1582
24	0.1074	0.2496	0.0094	0.1353	-0.0519	0.0348	-0.0822	0.0374	-0.0515	-0.1722	0.1179	-0.0144	0.2101	0.0317	0.0000	0.3192	-0.0058	-0.0009	0.2070	-0.0194	0.1619	7.1546	66.8238	20.2700
25	0.1407	0.0728	-0.0736	0.2049	-0.0439	0.0516	-0.0133	0.0763	-0.1117	-0.0186	-0.0021	-0.2486	0.4011	0.0015	-0.0019	0.5489	-0.0506	-0.0045	0.3441	-0.0312	0.1853	13.8910	71.1680	7.6983
26	0.0907	0.0980	-0.0129	0.0211	-0.0365	0.0754	-0.1633	-0.0866	-0.0798	0.0116	-0.0833	-0.1178	0.1169	0.2034	-0.0000	0.5027	-0.0236	0.0502	0.2893	0.0116	0.1930	14.7379	77.5966	10.6932
27	0.1719	-0.0828	0.0010	0.2332	-0.1727	0.0898	0.1123	0.1118	0.0527	-0.1584	0.0081	0.0619	0.0017	-0.0665	-0.0000	0.3047	-0.0309	0.0074	0.2204	0.0253	0.1539	2.5073	85.7736	20.0483
28	0.1079	0.0579	-0.0397	0.0561	0.0014	0.0107	0.0232	-0.1652	-0.1027	-0.4978	-0.0594	-0.1318	-0.7324	0.1720	-0.0002	0.4988	-0.1231	0.0706	0.3956	0.0134	0.3081	25.4952	99.6909	28.7836
29	0.2426	0.1076	0.1622	0.0598	0.0546	0.1125	0.2621	0.0939	0.0015	0.1699	0.0322	-0.0454	-0.1020	0.0816	0.0411	0.4430	-0.1131	0.0850	0.1818	0.0172	0.2253	14.9106	100.8377	33.0870
30	0.1189	0.0104	-0.0417	0.0888	-0.0429	0.0848	0.0779	0.1413	0.0716	0.0965	0.1525	-0.1468	0.0681	0.1040	0.0112	0.3165	-0.0389	-0.0024	0.2750	-0.0524	0.2020	17.6862	90.7325	23.3455
31	0.0878	0.0018	0.1976	0.0983	-0.1549	0.1512	-0.0548	0.0597	-0.0649	-0.0799	0.1403	-0.0960	-0.0490	0.0893	-0.0001	0.4076	-0.0748	0.0522	0.2480	-0.0009	0.2105	17.8317	93.4903	14.5648

Refine TLS group

Refine ID: X-RAY DIFFRACTION

ID	Beg auth asym ID	Beg auth seq ID	End auth asym ID	End auth seq ID	Refine TLS ID	Selection details
1	A	9	A	122	1	chain 'A' and (resid 9 through 122 )
2	A	123	A	247	2	chain 'A' and (resid 123 through 247 )
3	A	248	A	335	3	chain 'A' and (resid 248 through 335 )
4	B	9	B	122	4	chain 'B' and (resid 9 through 122 )
5	B	123	B	247	5	chain 'B' and (resid 123 through 247 )
6	B	248	B	335	6	chain 'B' and (resid 248 through 335 )
7	C	9	C	131	7	chain 'C' and (resid 9 through 131 )
8	C	132	C	335	8	chain 'C' and (resid 132 through 335 )
9	D	9	D	88	9	chain 'D' and (resid 9 through 88 )
10	D	89	D	106	10	chain 'D' and (resid 89 through 106 )
11	D	107	D	155	11	chain 'D' and (resid 107 through 155 )
12	D	156	D	247	12	chain 'D' and (resid 156 through 247 )
13	D	248	D	335	13	chain 'D' and (resid 248 through 335 )
14	E	9	E	106	14	chain 'E' and (resid 9 through 106 )
15	E	107	E	179	15	chain 'E' and (resid 107 through 179 )
16	E	180	E	247	16	chain 'E' and (resid 180 through 247 )
17	E	248	E	335	17	chain 'E' and (resid 248 through 335 )
18	F	9	F	122	18	chain 'F' and (resid 9 through 122 )
19	F	123	F	247	19	chain 'F' and (resid 123 through 247 )
20	F	248	F	335	20	chain 'F' and (resid 248 through 335 )
21	G	9	G	131	21	chain 'G' and (resid 9 through 131 )
22	G	132	G	335	22	chain 'G' and (resid 132 through 335 )
23	H	9	H	28	23	chain 'H' and (resid 9 through 28 )
24	H	29	H	88	24	chain 'H' and (resid 29 through 88 )
25	H	89	H	122	25	chain 'H' and (resid 89 through 122 )
26	H	123	H	155	26	chain 'H' and (resid 123 through 155 )
27	H	156	H	212	27	chain 'H' and (resid 156 through 212 )
28	H	213	H	231	28	chain 'H' and (resid 213 through 231 )
29	H	232	H	247	29	chain 'H' and (resid 232 through 247 )
30	H	248	H	274	30	chain 'H' and (resid 248 through 274 )
31	H	275	H	335	31	chain 'H' and (resid 275 through 335 )

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