PDB-5q0b: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosph...

ID or keywords:

Entry

Database: PDB / ID: 5q0b

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-(4-bromo-3-methyl-1,2-thiazol-5-yl)-3-(3-methylphenyl)sulfonylurea

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: 2.3 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-(4-bromo-3-methyl-1,2-thiazol-5-yl)-3-(3-methylphenyl)sulfonylurea
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	5q0b.cif.gz	495.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5q0b.ent.gz	408.4 KB	Display	PDB format
PDBx/mmJSON format	5q0b.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/q0/5q0b ftp://data.pdbj.org/pub/pdb/validation_reports/q0/5q0b	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	2wbd-2 2y5l-1 5q02-d 5pzu-d 5q07-2 5q0a-d 4mjo-1 5pzr-d 2fix-d 5pzs-d 5q07-1 5pzw-d 5pzv-d 2wbb-2 5pzx-1 5q04-1 2vt5-1 5pzx-2 2fhy-d 2wbb-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	#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)	67.471, 83.093, 276.415
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 156 or resid 158 through 335))
2	1	(chain B and (resid 9 through 156 or resid 158 through 335))
3	1	(chain C and (resid 9 through 156 or resid 158 through 335))
4	1	(chain D and (resid 9 through 156 or resid 158 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	GLY	GLY	(chain A and (resid 9 through 61 or resid 72 through 156 or resid 158 through 335))	A	A	9 - 61	10 - 62
1	2	LYS	LYS	GLY	GLY	(chain A and (resid 9 through 61 or resid 72 through 156 or resid 158 through 335))	A	A	72 - 156	73 - 157
1	3	ASN	ASN	SER	SER	(chain A and (resid 9 through 61 or resid 72 through 156 or resid 158 through 335))	A	A	158 - 335	159 - 336
2	1	ASP	ASP	GLY	GLY	(chain B and (resid 9 through 156 or resid 158 through 335))	B	B	9 - 156	10 - 157
2	2	ASN	ASN	SER	SER	(chain B and (resid 9 through 156 or resid 158 through 335))	B	B	158 - 335	159 - 336
3	1	ASP	ASP	GLY	GLY	(chain C and (resid 9 through 156 or resid 158 through 335))	C	C	9 - 156	10 - 157
3	2	ASN	ASN	SER	SER	(chain C and (resid 9 through 156 or resid 158 through 335))	C	C	158 - 335	159 - 336
4	1	ASP	ASP	GLY	GLY	(chain D and (resid 9 through 156 or resid 158 through 335))	D	D	9 - 156	10 - 157
4	2	ASN	ASN	SER	SER	(chain D and (resid 9 through 156 or resid 158 through 335))	D	D	158 - 335	159 - 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-96J / N-[(4-bromo-3-methyl-1,2-thiazol-5-yl)carbamoyl]-3-methylbenzene-1-sulfonamide Mass: 390.276 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₁₂BrN₃O₃S₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 764 / 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: 2.71 Å³/Da / Density % sol: 54.68 %
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: Oct 3, 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: 2.3→29.601 Å / Num. obs: 68516 / % possible obs: 97.75 %

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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: 2.3→29.601 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.02 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2078	3458	5.05 %
R_work	0.155	65058	-
obs	0.1576	68516	97.75 %

Solvent computation

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

Displacement parameters

B_iso max: 99.79 Å² / B_iso mean: 27.4293 Å² / B_iso min: 4.16 Å²

Refinement step

Cycle: final / Resolution: 2.3→29.601 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9776	0	84	764	10624
B_iso mean	-	-	25.94	35.74	-
Num. residues	-	-	-	-	1278

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10073
X-RAY DIFFRACTION	f_angle_d	0.912	13620
X-RAY DIFFRACTION	f_chiral_restr	0.057	1540
X-RAY DIFFRACTION	f_plane_restr	0.006	1743
X-RAY DIFFRACTION	f_dihedral_angle_d	10.945	6116

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	6061	X-RAY DIFFRACTION	8.999	TORSIONAL
1	2	B	6061	X-RAY DIFFRACTION	8.999	TORSIONAL
1	3	C	6061	X-RAY DIFFRACTION	8.999	TORSIONAL
1	4	D	6061	X-RAY DIFFRACTION	8.999	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 25

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.3-2.3315	0.2436	117	0.1664	1937	2054	74
2.3315-2.3648	0.2413	129	0.1745	2209	2338	86
2.3648-2.4001	0.2404	122	0.1685	2351	2473	89
2.4001-2.4376	0.2613	148	0.1648	2540	2688	97
2.4376-2.4775	0.2426	124	0.1606	2614	2738	100
2.4775-2.5202	0.2266	124	0.1561	2662	2786	100
2.5202-2.566	0.2053	139	0.1629	2594	2733	100
2.566-2.6154	0.2324	140	0.1653	2653	2793	100
2.6154-2.6687	0.2436	122	0.1683	2640	2762	100
2.6687-2.7267	0.229	129	0.1543	2624	2753	100
2.7267-2.7901	0.2015	118	0.1486	2664	2782	100
2.7901-2.8598	0.2009	141	0.1522	2634	2775	100
2.8598-2.937	0.2127	143	0.1531	2662	2805	100
2.937-3.0234	0.2083	151	0.1591	2605	2756	100
3.0234-3.1209	0.2278	129	0.1492	2666	2795	100
3.1209-3.2323	0.202	158	0.1494	2663	2821	100
3.2323-3.3615	0.215	157	0.1487	2651	2808	100
3.3615-3.5143	0.2253	163	0.1575	2595	2758	100
3.5143-3.6992	0.1876	147	0.1523	2673	2820	100
3.6992-3.9305	0.1865	164	0.1516	2654	2818	100
3.9305-4.2332	0.1855	126	0.1363	2697	2823	100
4.2332-4.6577	0.1706	142	0.1269	2706	2848	100
4.6577-5.3283	0.1671	125	0.1383	2729	2854	100
5.3283-6.7003	0.2215	148	0.1845	2750	2898	100
6.7003-29.603	0.213	152	0.1852	2885	3037	100

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	0.0565	-0.0237	-0.0073	0.0143	0.0062	0.0187	-0.0298	0.0748	-0.0116	0.0145	0.0123	0.0277	-0.0958	-0.0412	-0.0209	0.1223	-0.0093	0.0105	0.0943	0.0073	0.0728	14.8343	42.0863	15.9241
2	0.0139	-0.0102	-0.0101	0.0405	-0.0255	0.0383	-0.0572	0.0736	0.0864	-0.0153	0.031	-0.0555	-0.1485	0.0924	-0.0256	0.1183	-0.0613	0.0494	0.1571	-0.0018	0.1269	33.4802	43.9292	10.1078
3	0.0149	-0.0128	0.012	0.0907	0.0003	0.0175	0.0394	0.0624	0.0356	-0.0661	-0.012	-0.0681	-0.0311	0.0383	0.0528	0.1707	-0.1238	0.0942	0.178	0.0461	0.08	36.0334	45.8405	1.8472
4	0.0643	-0.0288	0.0127	0.0206	-0.0121	0.0617	-0.0255	-0.0212	-0.0808	0.0143	-0.0016	0.0088	-0.0236	0.0017	-0.047	0.0078	0.0017	-0.0103	0.0708	-0.0523	0.0863	36.1995	20.0615	36.822
5	0.01	0.0048	-0.0213	0.0138	-0.0098	0.077	0.0528	-0.0146	-0.0015	0.038	0.05	-0.0686	0	0.0687	0.0451	0.049	0.0271	-0.0236	0.1012	-0.0432	0.1303	42.3529	16.3983	29.3026
6	0.0025	-0.0108	-0.0132	0.0443	-0.0283	0.0237	0.0486	0.0855	-0.0054	-0.0074	0.0868	-0.0451	-0.0133	0.1286	0.1303	-0.0211	0.0272	0.1303	0.1633	-0.1579	0.0237	40.0727	20.9551	9.9754
7	0.0267	-0.0063	0.0068	0.0004	0.0003	0.0039	-0.0057	0.078	-0.0533	-0.0019	-0.0175	-0.0001	0.0099	0.0418	-0.0398	-0.0101	0.0246	0.0256	0.2355	-0.1149	0.1381	49.0294	16.8921	15.9613
8	0.0253	0.0242	-0.0168	0.0302	0.0051	0.0523	0.0148	0.0256	0.0449	-0.0482	0.015	-0.0246	-0.1292	0.0123	0.0425	0.1371	0.0024	0.0143	0.0549	-0.0023	0.074	16.0727	51.0435	39.9692
9	0.0206	-0.0026	-0.0117	0.0024	0.0053	0.0114	-0.0158	-0.0434	0.0189	0.0196	-0.0296	-0.0013	0.0465	0.0325	-0.0034	0.181	0.0063	0.0414	0.0542	-0.0119	0.1168	9.9388	55.3195	48.5603
10	0.0315	-0.0198	0.0292	0.0241	-0.0068	0.021	0.0018	0.0161	0.0262	-0.0303	0.0004	0.0482	-0.0181	-0.0693	-0	0.0743	0.0017	0.0087	0.0841	0.0057	0.0796	-4.519	42.1025	46.2052
11	0.0089	0.0173	-0.0047	0.0227	-0.0022	0.0111	-0.003	-0.0233	-0.0008	0.1067	0.0414	0.0022	-0.0585	-0.0723	0.015	0.0945	0.0265	0.0083	0.0773	0.0064	0.0675	-4.8454	49.6762	53.1207
12	0.0116	0.0021	-0.0038	0.0043	0.0018	0.0111	0.0012	0.0017	-0.102	-0.0209	-0.0146	-0.0328	0.0008	-0.0351	-0	0.0724	0.0042	-0.009	0.056	-0.0103	0.1175	11.7529	13.498	36.7251
13	0.0085	0.0036	0.0003	0.0015	0.003	0.0152	-0.0039	-0.0078	-0.0292	0.0056	0.0111	0.0081	-0.0397	-0.08	-0.0001	0.0993	-0.0005	0.0315	0.0898	0.0168	0.1332	3.4061	9.4914	42.9732
14	0.0208	0.012	0.0152	0.0326	-0.0108	0.0457	0.0272	-0.0244	-0.0295	0.0736	0.0097	-0.0355	0.0523	0.0103	0.0257	0.1207	-0.0041	0.0088	0.0983	0.0015	0.0886	5.6914	23.4905	56.9875
15	0.0106	-0.0039	-0.0038	0.0137	-0.0044	0.0046	0.0315	0.0175	-0.0347	0.0726	-0.0449	0.0475	0.0285	-0.0282	-0.0076	0.094	-0.0101	0.0152	0.0685	0.0028	0.0784	-1.3744	15.4697	57.8495

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 179 )	B	123 - 179
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 180 through 247 )	B	180 - 247
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 248 through 335 )	B	248 - 335
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 9 through 122 )	C	9 - 122
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 123 through 155 )	C	123 - 155
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 156 through 247 )	C	156 - 247
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 248 through 335 )	C	248 - 335
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 9 through 122 )	D	9 - 122
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 123 through 155 )	D	123 - 155
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 156 through 247 )	D	156 - 247
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 248 through 335 )	D	248 - 335

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Yorodumi