PDB-5q06: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosph...

ID or keywords:

Entry

Database: PDB / ID: 5q06

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-[4-(2-methyl-1,3-thiazol-4-yl)phenyl]sulfonylurea

Components

Fructose-1,6-bisphosphatase 1

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 / cellular response to magnesium ion / Gluconeogenesis / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.4 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-(5-bromo-1,3-thiazol-2-yl)-3-[4-(2-methyl-1,3- ...
Authors: Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G.

History

Deposition	Apr 18, 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	5q06.cif.gz	492.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5q06.ent.gz	406.1 KB	Display	PDB format
PDBx/mmJSON format	5q06.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5q06_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	5q06_full_validation.pdf.gz	1.5 MB	Display
Data in XML	5q06_validation.xml.gz	52 KB	Display
Data in CIF	5q06_validation.cif.gz	74.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q0/5q06 ftp://data.pdbj.org/pub/pdb/validation_reports/q0/5q06	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	5q0a-d 5q07-2 5pzy-1 2vt5-1 2fix-d 5q05-1 6lw2-d 2fie-d 5q08-2 2wbd-1 5pzx-1 3a29-d 5q08-1 5pzu-d 2fhy-d 5q03-1 5q07-1 5zwk-d 4mjo-1 2wbd-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)	67.506, 83.695, 278.843
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 37 or resid 39 through 61 or resid 72 through 335))
2	1	(chain B and (resid 9 through 37 or resid 39 through 335))
3	1	(chain C and (resid 9 through 37 or resid 39 through 61 or resid 72 through 335))
4	1	(chain D and (resid 9 through 37 or resid 39 through 335))

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	LEU	LEU	(chain A and (resid 9 through 37 or resid 39 through 61 or resid 72 through 335))	A	A	9 - 37	10 - 38
1	2	THR	THR	GLY	GLY	(chain A and (resid 9 through 37 or resid 39 through 61 or resid 72 through 335))	A	A	39 - 61	40 - 62
1	3	LYS	LYS	SER	SER	(chain A and (resid 9 through 37 or resid 39 through 61 or resid 72 through 335))	A	A	72 - 335	73 - 336
2	1	ASP	ASP	LEU	LEU	(chain B and (resid 9 through 37 or resid 39 through 335))	B	B	9 - 37	10 - 38
2	2	THR	THR	SER	SER	(chain B and (resid 9 through 37 or resid 39 through 335))	B	B	39 - 335	40 - 336
3	1	ASP	ASP	LEU	LEU	(chain C and (resid 9 through 37 or resid 39 through 61 or resid 72 through 335))	C	C	9 - 37	10 - 38
3	2	THR	THR	GLY	GLY	(chain C and (resid 9 through 37 or resid 39 through 61 or resid 72 through 335))	C	C	39 - 61	40 - 62
3	3	LYS	LYS	SER	SER	(chain C and (resid 9 through 37 or resid 39 through 61 or resid 72 through 335))	C	C	72 - 335	73 - 336
4	1	ASP	ASP	LEU	LEU	(chain D and (resid 9 through 37 or resid 39 through 335))	D	D	9 - 37	10 - 38
4	2	THR	THR	SER	SER	(chain D and (resid 9 through 37 or resid 39 through 335))	D	D	39 - 335	40 - 336

#1: Protein	Fructose-1,6-bisphosphatase 1 / 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-95V / N-[(5-bromo-1,3-thiazol-2-yl)carbamoyl]-4-(2-methyl-1,3-thiazol-4-yl)benzene-1-sulfonamide Mass: 459.361 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₁₁BrN₄O₃S₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 704 / 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: 2.76 Å³/Da / Density % sol: 55.43 %
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: 2.4→19.986 Å / Num. obs: 62733 / % possible obs: 99.98 %

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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: 2.4→19.986 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2338	3164	5.04 %
R_work	0.168	59569	-
obs	0.1713	62733	99.98 %

Solvent computation

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

Displacement parameters

B_iso max: 114.62 Å² / B_iso mean: 29.5649 Å² / B_iso min: 5.15 Å²

Refinement step

Cycle: final / Resolution: 2.4→19.986 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9729	0	100	704	10533
B_iso mean	-	-	35.84	34.6	-
Num. residues	-	-	-	-	1271

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	10037
X-RAY DIFFRACTION	f_angle_d	0.998	13572
X-RAY DIFFRACTION	f_chiral_restr	0.06	1532
X-RAY DIFFRACTION	f_plane_restr	0.007	1735
X-RAY DIFFRACTION	f_dihedral_angle_d	12.822	6086

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	6069	X-RAY DIFFRACTION	10.498	TORSIONAL
1	2	B	6069	X-RAY DIFFRACTION	10.498	TORSIONAL
1	3	C	6069	X-RAY DIFFRACTION	10.498	TORSIONAL
1	4	D	6069	X-RAY DIFFRACTION	10.498	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 23 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
2.4-2.4358	0.3096	129	0.2171	2556	2685
2.4358-2.4738	0.3023	147	0.2213	2536	2683
2.4738-2.5143	0.3095	138	0.2172	2553	2691
2.5143-2.5575	0.2997	121	0.2162	2567	2688
2.5575-2.604	0.2894	136	0.213	2559	2695
2.604-2.6539	0.2864	146	0.2023	2534	2680
2.6539-2.708	0.2836	145	0.1985	2573	2718
2.708-2.7667	0.2645	118	0.1924	2558	2676
2.7667-2.8309	0.2567	127	0.187	2586	2713
2.8309-2.9015	0.2624	150	0.1898	2542	2692
2.9015-2.9797	0.2778	140	0.1918	2568	2708
2.9797-3.0671	0.3214	126	0.1938	2604	2730
3.0671-3.1657	0.2694	136	0.1848	2566	2702
3.1657-3.2784	0.2549	146	0.1735	2550	2696
3.2784-3.409	0.2459	123	0.1635	2597	2720
3.409-3.5633	0.2235	134	0.1509	2602	2736
3.5633-3.75	0.2069	134	0.1498	2589	2723
3.75-3.9832	0.2016	145	0.1409	2632	2777
3.9832-4.288	0.1822	133	0.1354	2585	2718
4.288-4.7144	0.1755	152	0.1206	2600	2752
4.7144-5.3849	0.1798	130	0.1315	2655	2785
5.3849-6.7408	0.1988	148	0.1716	2685	2833
6.7408-19.9864	0.1959	160	0.1663	2772	2932

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	0.0839	-0.0063	0.0081	0.0268	0.0318	0.0685	-0.0208	0.0555	-0.0099	0.0273	-0.0101	0.0263	-0.1052	-0.0744	-0.0394	0.0963	-0.0056	0.0179	0.0457	-0.009	0.0394	16.0935	43.2922	16.4848
2	0.0407	0.0245	-0.0344	0.037	-0.0276	0.0326	-0.0324	0.0824	0.0907	-0.0628	0.0103	-0.0346	-0.0576	0.0313	-0.0489	0.1183	-0.0292	0.042	0.1287	0.0065	0.0709	34.427	43.536	11.1363
3	0.016	-0.0158	0.01	0.0088	-0.0097	0.0113	0.0167	0.0218	0.0071	-0.0347	0.0106	0.0233	0.0031	0.1113	0.0008	0.1508	-0.0692	0.0151	0.1571	0.0001	0.112	37.0613	45.7782	2.8682
4	0.0738	0.0151	-0.0451	0.033	-0.0364	0.0595	0.0022	-0.0621	-0.0774	0.0556	-0.0384	0.0591	-0.0276	0.035	-0.0247	0.052	0.0056	-0.0184	0.0767	-0.0164	0.0823	36.4239	19.0585	37.231
5	0.0298	-0.0204	-0.0058	0.0083	-0.0017	0.0102	0.0229	0.0735	-0.0468	-0.0062	0.0154	0.0005	-0.0089	0.0833	0.0444	0.054	-0.0155	0.0213	0.1364	-0.047	0.0814	41.5633	18.3917	18.9128
6	0.0004	0.0047	-0.001	0.0562	-0.0213	0.0086	0.0267	0.0416	-0.0174	0.0795	0.0182	0.0263	0.0002	0.1183	0.0206	0.0788	0.0163	0.0056	0.1877	-0.0503	0.1022	49.5566	16.1791	16.302
7	0.0066	0.0005	0.0005	0.0011	-0.002	0.0058	0.0077	-0.0052	0.0122	-0.0141	-0.0038	0.0019	-0.0184	-0.0033	0.0006	0.1627	0.0883	-0.0389	0.0831	0.0318	0.0906	6.6326	53.53	25.2106
8	0.0097	-0.0012	0.0177	0.0272	0.018	0.0136	-0.0075	-0.0067	0.0175	0.012	0.0393	0.0471	-0.0971	0.027	0.0324	0.1183	0.0395	0.0609	-0.0285	-0.0306	0.0792	15.146	50.5074	45.4838
9	0.0121	-0.0004	0.0136	0.0499	-0.0021	0.0077	0.0041	0.0049	0.0494	-0.0206	0.0231	0.0773	-0.0266	-0.0799	0.0007	0.0876	0.0119	0.0185	0.1288	-0.0026	0.1118	-5.8458	39.6513	47.4394
10	0.0106	0.0123	0.0042	0.0118	-0.0048	0.0603	-0.0175	-0.0207	0.017	0.0731	0.0206	-0.0466	-0.0113	-0.0826	0.0031	0.08	0.0325	0.0137	0.079	-0.0109	0.0803	-4.7801	48.8045	53.7233
11	0.0016	0	0.0012	0.0008	-0.0003	0.0025	-0.0301	-0.0163	-0.0243	-0.0029	-0.0093	-0.0166	0.009	0.0185	0	0.1844	0.0116	0.0036	0.1278	0.0337	0.2707	27.611	9.2857	47.1145
12	0.0265	-0.0058	0.011	0.0162	-0.0004	0.0163	-0.0205	0.0104	-0.0341	-0.0235	-0.0079	-0.0028	0.0085	-0.0034	-0.0271	0.0828	0.0103	0.0273	0.0607	-0.0234	0.0867	10.8195	19.0553	33.2027
13	0.0006	0.0001	-0.0014	0.0006	0.0002	0.0003	0.0162	0.0391	-0.0129	0.0055	-0.021	0.0294	0.0019	-0.0065	0.0014	0.0573	0.0271	0.0082	0.0726	-0.0033	0.1422	5.4085	5.5637	37.0245
14	0.0091	-0.0007	-0.005	0.0152	0.0254	0.0426	-0.0463	-0.0002	-0.0377	-0.042	0.0141	-0.009	-0.081	-0.0347	-0.0411	0.0775	0.0516	0.0183	-0.0081	0.012	0.0908	7.2988	11.0049	45.9668
15	0.0186	0.0094	0.0149	0.0251	0.0138	0.0112	0.0167	0.0079	-0.0287	0.002	-0.0117	-0.0566	-0.0115	0.0125	0.0249	0.045	-0.0174	0.0048	0.0868	0.029	0.0867	15.0403	22.5554	54.1951
16	0.003	0.0031	0.002	0.0036	0.0007	0.0021	-0.0152	0.0411	0.0152	0.0237	0.0418	-0.0001	0.0154	-0.0028	0.0001	0.1237	-0.0301	0.0346	0.154	0.0193	0.1059	-10.8355	24.798	64.7444
17	0.0078	0.0033	-0.0065	0.0208	-0.0027	0.007	0.016	-0.0192	0.0524	0.0264	0.0118	0.0005	-0.0269	0.0191	0.0105	0.1053	-0.028	0.0133	0.0581	-0.0175	0.0658	-0.0242	20.4695	57.8665
18	0.0065	0.0046	-0.0025	0.0148	0.0021	0.0014	-0.0266	0.0095	-0.0093	0.0146	0.0035	0.0639	0.0078	-0	-0.0011	0.1416	-0.0071	0.0306	0.1022	0.036	0.1164	-2.7022	11.6947	61.835

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 247 )	A	123 - 247
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 248 through 335 )	A	248 - 335
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 9 through 122 )	B	9 - 122
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 123 through 247 )	B	123 - 247
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 248 through 335 )	B	248 - 335
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 9 through 28 )	C	9 - 28
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 29 through 170 )	C	29 - 170
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 171 through 247 )	C	171 - 247
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 248 through 335 )	C	248 - 335
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 9 through 28 )	D	9 - 28
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 29 through 88 )	D	29 - 88
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 89 through 122 )	D	89 - 122
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 123 through 179 )	D	123 - 179
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 180 through 212 )	D	180 - 212
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 213 through 231 )	D	213 - 231
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 232 through 290 )	D	232 - 290
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 291 through 335 )	D	291 - 335

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Structure viewers

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Viewer log

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This page

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This web site

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Open data

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Basic information

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Validation report

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Group deposition

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Phasing

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Processing

+
About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi