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

ID or keywords:

Entry

Database: PDB / ID: 5pzr

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-(3-chlorophenyl)sulfonyl-3-[3-[3-[(3-chlorophenyl)sulfonylcarbamoylamino]propoxy]propyl]urea

Components

Fructose-1,6-bisphosphatase 1

Fructose 1,6-bisphosphatase

Keywords

HYDROLASE/HYDROLASE inhibitor / D3R docking / HYDROLASE-HYDROLASE inhibitor complex

Function / homology

Function and homology information

cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / negative regulation of Ras protein signal transduction / fructose 1,6-bisphosphate metabolic process / cellular response to magnesium ion / fructose 6-phosphate metabolic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 Å

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-(3-chlorophenyl)sulfonyl-3-[3-[3-[(3-chlorophenyl) ...
Authors: Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G.

History

Deposition	Apr 11, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 9, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 16, 2019	Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.2	Feb 6, 2019	Group: Data collection / Database references / Structure summary Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3	Feb 10, 2021	Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4	Mar 6, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5pzr.cif.gz	503.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5pzr.ent.gz	413.5 KB	Display	PDB format
PDBx/mmJSON format	5pzr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pz/5pzr ftp://data.pdbj.org/pub/pdb/validation_reports/pz/5pzr	HTTPS FTP

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Group deposition

ID	G_1002030 (23 entries) 5pzq 5pzr 5pzs 5pzt 5pzu 5pzv 5pzw 5pzx 5pzy 5pzz
Title	Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with allosteric inhibitors
Type	undefined
Description	Fructose-1,6-bisphosphatase 1 with inhibitors

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Related structure data

Similar structure data	2y5l-1 2wbd-2 5pzs-d 5q04-1 4fbp-d 2fix-d 5pzv-d 5q02-d 3kc0-d 5pzy-2 5pzz-1 5q0b-d 2y5l-2 5pzx-2 5q08-1 5q07-2 5pzx-1 5pzu-d 4mjo-1 5q03-2 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	#50 - Feb 2004 Glycolytic Enzymes similarity (1)

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

hetero molecules

149 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	67.306, 83.148, 277.665
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 9 through 61 or resid 72 through 335))
2	1	chain B
3	1	(chain C and (resid 9 through 61 or resid 72 through 335))
4	1	chain D

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASP	ASP	GLY	GLY	(chain A and (resid 9 through 61 or resid 72 through 335))	A	A	9 - 61	10 - 62
1	2	LYS	LYS	SER	SER	(chain A and (resid 9 through 61 or resid 72 through 335))	A	A	72 - 335	73 - 336
2	1	ASP	ASP	SER	SER	chain B	B	B	9 - 335	10 - 336
3	1	ASP	ASP	GLY	GLY	(chain C and (resid 9 through 61 or resid 72 through 335))	C	C	9 - 61	10 - 62
3	2	LYS	LYS	SER	SER	(chain C and (resid 9 through 61 or resid 72 through 335))	C	C	72 - 335	73 - 336
4	1	ASP	ASP	SER	SER	chain D	D	D	9 - 335	10 - 336

#1: Protein	Fructose-1,6-bisphosphatase 1 / Fructose 1,6-bisphosphatase / Growth-inhibiting protein 17 / cDNA FLJ75786 / highly similar to Homo sapiens fructose-1 / 6- ...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.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FBP1, hCG_1640493 / Production host: Escherichia coli (E. coli) References: UniProt: Q2TU34, UniProt: P09467*PLUS, fructose-bisphosphatase
#2: Chemical	ChemComp-93S / N,N'-{oxybis[(propane-3,1-diyl)carbamoyl]}bis(3-chlorobenzene-1-sulfonamide) Mass: 567.463 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₄Cl₂N₄O₇S₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1204 / 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: 2.72 Å³/Da / Density % sol: 54.81 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M HEPES pH 7.0, 0.1M AMMONIUM ACETATE, 12% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.987 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 17, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 1.9→29.833 Å / Num. obs: 115654 / % possible obs: 93.49 %

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification	NB
PHENIX	1.11.1_2575	refinement
PDB_EXTRACT	3.23	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→29.833 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2176	5812	5.03 %
R_work	0.178	109842	-
obs	0.1801	115654	93.49 %

Solvent computation

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

Displacement parameters

B_iso max: 102.52 Å² / B_iso mean: 24.551 Å² / B_iso min: 3.91 Å²

Refinement step

Cycle: final / Resolution: 1.9→29.833 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9729	0	70	1204	11003
B_iso mean	-	-	27.07	36.28	-
Num. residues	-	-	-	-	1271

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	9973
X-RAY DIFFRACTION	f_angle_d	0.871	13470
X-RAY DIFFRACTION	f_chiral_restr	0.056	1528
X-RAY DIFFRACTION	f_plane_restr	0.005	1719
X-RAY DIFFRACTION	f_dihedral_angle_d	12.098	6072

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	6094	X-RAY DIFFRACTION	9.97	TORSIONAL
1	2	B	6094	X-RAY DIFFRACTION	9.97	TORSIONAL
1	3	C	6094	X-RAY DIFFRACTION	9.97	TORSIONAL
1	4	D	6094	X-RAY DIFFRACTION	9.97	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9-1.9216	0.3964	122	0.3267	2469	2591	63
1.9216-1.9442	0.3435	154	0.3169	2626	2780	68
1.9442-1.9679	0.3433	165	0.2929	2703	2868	71
1.9679-1.9928	0.3026	147	0.2773	2914	3061	75
1.9928-2.019	0.3191	164	0.2767	3098	3262	80
2.019-2.0467	0.3187	171	0.2532	3185	3356	83
2.0467-2.0759	0.2883	166	0.2442	3454	3620	89
2.0759-2.1069	0.2963	192	0.231	3602	3794	92
2.1069-2.1398	0.2545	179	0.2297	3667	3846	94
2.1398-2.1749	0.2788	202	0.2117	3653	3855	95
2.1749-2.2124	0.265	199	0.2021	3697	3896	97
2.2124-2.2526	0.2594	226	0.1886	3908	4134	100
2.2526-2.2959	0.2408	193	0.1855	3864	4057	100
2.2959-2.3427	0.2301	226	0.1833	3870	4096	100
2.3427-2.3937	0.2422	205	0.1762	3903	4108	100
2.3937-2.4493	0.2415	190	0.1752	3902	4092	100
2.4493-2.5105	0.225	181	0.1778	3932	4113	100
2.5105-2.5784	0.2222	198	0.1741	3895	4093	100
2.5784-2.6542	0.231	198	0.1676	3874	4072	100
2.6542-2.7398	0.2044	202	0.1651	3918	4120	100
2.7398-2.8377	0.1823	202	0.1637	3919	4121	100
2.8377-2.9512	0.2282	218	0.1631	3920	4138	100
2.9512-3.0854	0.1827	210	0.1661	3928	4138	100
3.0854-3.2478	0.1962	229	0.1507	3899	4128	100
3.2478-3.4511	0.1732	214	0.1472	3949	4163	100
3.4511-3.7171	0.1662	214	0.1475	3935	4149	100
3.7171-4.0903	0.1833	212	0.1431	3959	4171	100
4.0903-4.6802	0.1611	226	0.1388	3983	4209	100
4.6802-5.8891	0.1945	202	0.157	4057	4259	100
5.8891-29.8367	0.217	205	0.1913	4159	4364	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	0.0552	0.0067	-0.0018	0.007	-0.0107	0.0139	-0.0066	0.0387	0.0239	0.0316	0.033	0.0287	-0.1233	-0.0486	0.0016	0.1302	0.018	0.0172	0.0733	0.0083	0.069	16.1075	43.0544	16.4285
2	0.0095	0.0091	0.0049	0.0056	0.003	0.0045	-0.0129	0.0678	-0.0222	-0.037	-0.0092	0.0044	-0.0605	0.0054	-0	0.1764	0.0321	0.0073	0.1413	0.0175	0.0877	20.5587	45.5	6.3344
3	0.027	0.0283	-0.0247	0.0482	-0.0376	0.0422	-0.0411	0.0875	0.0657	-0.0546	-0.0081	-0.0803	-0.084	0.0929	-0.1092	0.1039	-0.098	0.0823	0.1566	-0.0028	0.0982	39.2623	42.4692	12.7647
4	0.0338	-0.0458	0.0039	0.0636	-0.0109	0.0014	0.0175	0.0824	0.022	-0.0918	-0.0127	-0.0814	-0.0294	0.0284	0.0123	0.1388	-0.089	0.0493	0.1985	0.0009	0.107	36.9027	45.4933	2.8055
5	0.1242	-0.0302	-0.0078	0.0138	-0.0182	0.0578	0.0212	-0.0569	-0.1088	0.0415	0.0231	0.0309	0.0149	0.0252	0.0678	0.0357	0.0193	0.0047	0.0749	-0.0291	0.0757	36.3863	18.8415	36.9978
6	0.0089	0.0033	0.0038	0.0022	0.0068	0.0204	0.0187	0.0035	0.0173	0.004	0.0253	-0.0177	-0.019	0.0493	0.0306	0.0316	0.025	0.0357	0.1249	-0.0453	0.1324	46.4719	16.6082	32.5332
7	0.0562	-0.0296	-0.0391	0.0165	0.0181	0.0309	0.0209	0.1053	-0.0666	-0.0375	0.0173	-0.0183	0.0173	0.1422	0.0327	0.0222	0.0452	0.0961	0.1505	-0.1282	0.0296	39.6421	18.8225	13.871
8	0.0054	0.0031	0.0118	0.0717	-0.0073	0.0343	-0.0216	0.0607	-0.072	0.0196	-0.0436	-0.0525	0.0346	0.0656	-0.1061	0.0329	0.0855	0.0327	0.2029	-0.0934	0.0796	49.47	16.0306	16.1785
9	0.0266	-0.004	-0.0032	0.0308	0.0324	0.0254	0.0327	0.0061	0.0611	-0.0608	0.0263	-0.0141	-0.0846	0.0011	0.0259	0.1186	0.0136	0.0335	0.0533	-0.0028	0.082	16.0382	48.5063	41.565
10	0.0438	-0.0148	0.0305	0.0616	0.0166	0.0532	0.0536	0.0056	0.0537	0.0262	-0.0333	0.0444	-0.0733	-0.0813	0.0112	0.1083	0.02	0.0242	0.0686	-0.0034	0.0715	-1.3241	45.1227	48.2857
11	0.0094	0.0009	0.0001	0.0044	0.0028	0.0127	0.0186	-0.0048	0.0099	0.0485	0.0058	0.0464	-0.0432	-0.0114	0.0239	0.1143	0.0808	0.0293	0.0966	-0.005	0.122	-8.4786	51.392	55.0322
12	0.0047	0.0052	-0.001	0.0065	0.0013	0.0046	0.0056	-0.0097	-0.0227	-0.0076	-0.009	-0.0262	-0.0074	0.0121	0	0.1543	0.0682	0.0174	0.1603	0.0016	0.2404	27.4809	9.1877	46.9945
13	0.0189	0.0115	-0.0003	0.0058	-0.0025	0.0125	-0.008	0.0291	-0.0509	-0.0067	0.0257	-0.0172	0.0109	0.0164	0.0047	0.0573	0.005	0.0142	0.0626	-0.0128	0.0511	10.7237	18.9856	32.9616
14	0.0011	0.0004	0.0008	0.0011	-0.0013	0.0021	0.0046	0.0049	-0.0202	-0.021	0.0015	0.0099	0.0143	-0.0395	-0	0.1307	0.0224	0.0035	0.0663	-0.0059	0.1448	3.3005	4.7876	35.5171
15	0.0226	0.0225	0.0205	0.0432	-0.0003	0.0423	0.015	0.0289	-0.0462	-0.0371	0.0123	-0.0138	0.018	-0.0184	0.0169	0.0975	0.0092	0.0446	0.0229	0.0145	0.1141	5.2142	7.6059	41.5215
16	0.0055	0.0041	-0.0004	0.0031	0.0033	0.007	-0.0185	0.0142	-0.0692	-0.0176	-0.0101	0.0022	0.0035	0.0088	-0.0002	0.0632	0.02	-0.0029	0.0349	-0.0043	0.0611	12.5193	14.639	49.6021
17	0.0172	-0.0043	0.0028	0.0288	0.0235	0.016	0.0635	0.01	-0.0148	0.0486	0.0236	-0.0178	0.0159	0.0017	0.0114	0.1085	0.0058	0.0243	0.101	0.0091	0.0939	15.004	22.3173	53.9565
18	0.0133	-0.0046	-0.0011	0.0092	0.0013	0.0004	0.0097	0.0386	0.0113	0.03	0.0158	-0.0084	0.0091	-0.0402	0.017	0.126	-0.0163	0.061	0.0904	0.0332	0.1069	-10.8108	24.5217	64.4329
19	0.0052	-0.0036	-0.0003	0.0027	0.001	0.001	0.023	0.0034	-0.0093	0.0486	-0.0079	0.0067	-0.0015	0.0142	0	0.1493	-0.0007	0.0357	0.1059	0.017	0.0731	-1.1872	30.2475	66.3235
20	0.001	-0.0001	-0.0008	-0.0008	0.0002	0.0052	0.0101	-0.0091	0.0081	-0.001	-0.0393	0.0422	0.0111	-0.017	-0.0011	0.0979	-0.0066	0.0226	0.0686	-0.0151	0.0809	-1.7858	20.2522	56.0999
21	0.016	-0.0006	0.0058	0.0034	-0.0033	0.0107	0.0062	-0.0527	-0.0731	0.0418	0.0043	0.0428	0.0358	-0.0185	0.0075	0.0803	-0.0193	0.0308	0.0786	0.0165	0.0866	-0.8484	11.5607	58.8587

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 122 )	A	9 - 122
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 123 through 155 )	A	123 - 155
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 156 through 247 )	A	156 - 247
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 248 through 335 )	A	248 - 335
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 9 through 122 )	B	9 - 122
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 123 through 155 )	B	123 - 155
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 156 through 247 )	B	156 - 247
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 248 through 335 )	B	248 - 335
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 9 through 131 )	C	9 - 131
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 132 through 290 )	C	132 - 290
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 291 through 335 )	C	291 - 335
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 9 through 28 )	D	9 - 28
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 29 through 88 )	D	29 - 88
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 89 through 106 )	D	89 - 106
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 107 through 155 )	D	107 - 155
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 156 through 179 )	D	156 - 179
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 180 through 212 )	D	180 - 212
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 213 through 231 )	D	213 - 231
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 232 through 247 )	D	232 - 247
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 248 through 274 )	D	248 - 274
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 275 through 335 )	D	275 - 335

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