BMRBj - BMREntryMaster

Found 1 Document (0.656 seconds)

BMRB: 30478

6DO7

NMR solution structure of wild type hFABP1 in the presence of GW7647

Authors

Scanlon, M.J., Mohanty, B., Doak, B.C., Patil, R.

Assembly

Fatty acid-binding protein, liver

Entity

1. Fatty acid-binding protein, liver, entity 1 (polymer), 135 monomers, 15201.25 Da Detail

HHHHHHVAMS FSGKYQLQSQ ENFEAFMKAI GLPEELIQKG KDIKGVSEIV QNGKHFKFTI TAGSKVIQNE FTVGEECELE TMTGEKVKTV VQLEGDNKLV TTFKNIKSVT ELNGDIITNT MTLGDIVFKR ISKRI

2. Fatty acid-binding protein, liver, entity 2VN (non-polymer), 502.752 Da

Total weight

15704.002 Da

Max. entity weight

15201.25 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

restraint energy minimization

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.3 %, Completeness: 84.5 %, Completeness (bb): 80.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.5 % (1361 of 1610)	90.1 % (754 of 837)	74.6 % (466 of 625)	95.3 % (141 of 148)
Backbone	80.7 % (652 of 808)	92.9 % (260 of 280)	67.3 % (265 of 394)	94.8 % (127 of 134)
Sidechain	89.1 % (825 of 926)	88.7 % (494 of 557)	89.3 % (317 of 355)	100.0 % (14 of 14)
Aromatic	76.7 % (89 of 116)	77.6 % (45 of 58)	75.9 % (44 of 58)
Methyl	94.9 % (148 of 156)	94.9 % (74 of 78)	94.9 % (74 of 78)

1. entity 1

HHHHHHVAMS FSGKYQLQSQ ENFEAFMKAI GLPEELIQKG KDIKGVSEIV QNGKHFKFTI TAGSKVIQNE FTVGEECELE TMTGEKVKTV VQLEGDNKLV TTFKNIKSVT ELNGDIITNT MTLGDIVFKR ISKRI

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.5, Details 0.5 mM [U-15N13C] hFABP1 wild type, 0.5 mM unlabelled GW7647, 20 mM sodium phosphate, 50 mM sodium chloride, 1 % D6 DMSO, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	hFABP1 wild type	[U-15N13C]	0.5 mM
2	GW7647	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	DMSO	D6	1 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.5, Details 1 mM [U-2H,15N13C] hFABP1 wild type, 1 mM unlabelled GW7647, 50 mM sodium chloride, 20 mM sodium phosphate, 1 % D6 DMSO, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	hFABP1 wild type	[U-2H,15N13C]	1 mM
7	GW7647	natural abundance	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	DMSO	D6	1 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.07 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 6DRG, Strand ID: A Detail

Release date

2018-06-28

Citation

A ligand-induced structural change in fatty acid-binding protein 1 is associated with potentiation of peroxisome proliferator-activated receptor α agonists
Patil, R., Mohanty, B., Liu, B., Chandrashekaran, I.R., Headey, S.J., Williams, M.L., Clements, C.S., Ilyichova, O., Doak, B.C., Genissel, P., Weaver, R.J., Vuillard, L., Halls, M.L., Porter, C., Scanlon, M.J.
J. Biol. Chem. (2018), 294, 3720-3734, PubMed 30598509 , DOI 10.1074/jbc.RA118.006848 , Abstract

Related entities 1. Fatty acid-binding protein, liver, entity 1, : 1 : 2 : 26 : 197 entities Detail

Interaction partners 1. Fatty acid-binding protein, liver, entity 1, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.5, Details 0.5 mM [U-15N13C] hFABP1 wild type, 0.5 mM unlabelled GW7647, 20 mM sodium phosphate, 50 mM sodium chloride, 1 % D6 DMSO, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	hFABP1 wild type	[U-15N13C]	0.5 mM
2	GW7647	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	DMSO	D6	1 %

2 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	hFABP1 wild type	[U-15N13C]	0.5 mM
2	GW7647	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	DMSO	D6	1 %

3 3D 15N-resolved [1H,1H]-NOESY

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	hFABP1 wild type	[U-15N13C]	0.5 mM
2	GW7647	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	DMSO	D6	1 %

4 3D 13Cali resolved [1H,1H]-NOESY

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	hFABP1 wild type	[U-15N13C]	0.5 mM
2	GW7647	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	DMSO	D6	1 %

5 3D 13Caro resolved [1H,1H]-NOESY

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	hFABP1 wild type	[U-15N13C]	0.5 mM
2	GW7647	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	DMSO	D6	1 %

6 2D F1-edited, F2-13C,15N-filtered [1H,1H] NOESY

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	hFABP1 wild type	[U-15N13C]	0.5 mM
2	GW7647	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	DMSO	D6	1 %

7 3D F1-13C,15N-filtered, F2-13Cali edited [1H,1H] NOESY

Instrument

Bruker AVANCE III - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	hFABP1 wild type	[U-15N13C]	0.5 mM
2	GW7647	natural abundance	0.5 mM
3	sodium phosphate	natural abundance	20 mM
4	sodium chloride	natural abundance	50 mM
5	DMSO	D6	1 %

8 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 5.5, Details 1 mM [U-2H,15N13C] hFABP1 wild type, 1 mM unlabelled GW7647, 50 mM sodium chloride, 20 mM sodium phosphate, 1 % D6 DMSO, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
6	hFABP1 wild type	[U-2H,15N13C]	1 mM
7	GW7647	natural abundance	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	DMSO	D6	1 %

9 2D F1, F2-13C,15N-filtered [1H,1H] NOESY

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	hFABP1 wild type	[U-2H,15N13C]	1 mM
7	GW7647	natural abundance	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	DMSO	D6	1 %

10 2D F1-edited, F2-13C,15N-filtered [1H,1H] NOESY

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	hFABP1 wild type	[U-2H,15N13C]	1 mM
7	GW7647	natural abundance	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	DMSO	D6	1 %

11 3D F1-13C,15N-filtered, F2-15N edited [1H,1H] NOESY

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	hFABP1 wild type	[U-2H,15N13C]	1 mM
7	GW7647	natural abundance	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	DMSO	D6	1 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_30478_6do7.nef
Input source #2: Coordindates	6do7.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

----------------10--------20--------30--------40--------50--------60--------70--------80--------90--
HHHHHHVAMSFSGKYQLQSQENFEAFMKAIGLPEELIQKGKDIKGVSEIVQNGKHFKFTITAGSKVIQNEFTVGEECELETMTGEKVKTVVQLEGDNKLV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
HHHHHHVAMSFSGKYQLQSQENFEAFMKAIGLPEELIQKGKDIKGVSEIVQNGKHFKFTITAGSKVIQNEFTVGEECELETMTGEKVKTVVQLEGDNKLV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----100-------110-------120-------
TTFKNIKSVTELNGDIITNTMTLGDIVFKRISKRI
|||||||||||||||||||||||||||||||||||
TTFKNIKSVTELNGDIITNTMTLGDIVFKRISKRI
-------110-------120-------130-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	135	0	0	100.0

Content subtype: combined_30478_6do7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1366		96.3 (chain: A, length: 135)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2957 (1)	noe	94.8 (chain: A, length: 135)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 135, Sequence coverage: 96.3%
- Total number of assignments
  - ¹³C chemical shifts: 449
  - ¹H chemical shifts: 772
  - ¹⁵N chemical shifts: 145
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
122	ARG	HH11	6.818
122	ARG	HH21	6.879
122	ARG	NH1	66.697
122	ARG	NH2	66.84

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	625	449	71.8
¹H chemical shifts	837	770	92.0
¹⁵N chemical shifts	150	143	95.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	270	130	48.1
¹H chemical shifts	280	266	95.0
¹⁵N chemical shifts	134	127	94.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	355	319	89.9
¹H chemical shifts	557	504	90.5
¹⁵N chemical shifts	16	16	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	82	80	97.6
¹H chemical shifts	82	80	97.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	58	42	72.4
¹H chemical shifts	58	42	72.4

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 135, Sequence coverage: 94.8%
- Total number of restraints: 2957
- Weight of restraints: 1.0 (2957)
- Potential type of restraints: upper-bound-parabolic (2957)
- Range of distance target values: 2.4, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords GW7647, hLFABP

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Found 1 Document (0.656 seconds)

BMRB: 30478

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Fatty acid-binding protein, liver, entity 1, : 1 : 2 : 26 : 197 entities Detail

Interaction partners 1. Fatty acid-binding protein, liver, entity 1, : 2 interactors Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 3 contents Detail