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- PDB-6aq1: The crystal structure of human FABP3 -

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Basic information

Entry
Database: PDB / ID: 6aq1
TitleThe crystal structure of human FABP3
ComponentsFatty acid-binding protein, heart
KeywordsTRANSPORT PROTEIN / human / FABP3
Function / homology
Function and homology information


positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / oleic acid binding / phospholipid homeostasis / long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport ...positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / oleic acid binding / phospholipid homeostasis / long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport / brown fat cell differentiation / cytoskeletal protein binding / cholesterol homeostasis / negative regulation of cell population proliferation / extracellular space / extracellular exosome / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PALMITIC ACID / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.40000091001 Å
AuthorsHsu, H.C. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01 DA035923 United States
CitationJournal: Eur J Med Chem / Year: 2018
Title: SAR studies on truxillic acid mono esters as a new class of antinociceptive agents targeting fatty acid binding proteins.
Authors: Yan, S. / Elmes, M.W. / Tong, S. / Hu, K. / Awwa, M. / Teng, G.Y.H. / Jing, Y. / Freitag, M. / Gan, Q. / Clement, T. / Wei, L. / Sweeney, J.M. / Joseph, O.M. / Che, J. / Carbonetti, G.S. / ...Authors: Yan, S. / Elmes, M.W. / Tong, S. / Hu, K. / Awwa, M. / Teng, G.Y.H. / Jing, Y. / Freitag, M. / Gan, Q. / Clement, T. / Wei, L. / Sweeney, J.M. / Joseph, O.M. / Che, J. / Carbonetti, G.S. / Wang, L. / Bogdan, D.M. / Falcone, J. / Smietalo, N. / Zhou, Y. / Ralph, B. / Hsu, H.C. / Li, H. / Rizzo, R.C. / Deutsch, D.G. / Kaczocha, M. / Ojima, I.
History
DepositionAug 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid-binding protein, heart
B: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2208
Polymers30,3232
Non-polymers8976
Water6,521362
1
A: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5143
Polymers15,1611
Non-polymers3522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7065
Polymers15,1611
Non-polymers5454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.504, 52.904, 55.510
Angle α, β, γ (deg.)90.000, 97.453, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLYSLYS(chain A and (resseq 2:22 or resseq 24:27 or resseq...AA2 - 225 - 25
12LEULEUVALVAL(chain A and (resseq 2:22 or resseq 24:27 or resseq...AA24 - 2627 - 29
13ALAALAARGARG(chain A and (resseq 2:22 or resseq 24:27 or resseq...AA29 - 3132 - 34
14VALVALVALVAL(chain A and (resseq 2:22 or resseq 24:27 or resseq...AA3336
15METMETILEILE(chain A and (resseq 2:22 or resseq 24:27 or resseq...AA36 - 6339 - 66
16PHEPHEGLNGLN(chain A and (resseq 2:22 or resseq 24:27 or resseq...AA65 - 10168 - 104
17THRTHRARGARG(chain A and (resseq 2:22 or resseq 24:27 or resseq...AA103 - 107106 - 110
18LEULEUTYRTYR(chain A and (resseq 2:22 or resseq 24:27 or resseq...AA109 - 129112 - 132
19ALAALAALAALA(chain A and (resseq 2:22 or resseq 24:27 or resseq...AA133136
21VALVALLYSLYS(chain B and (resseq 2:22 or resseq 24:27 or resseq...BB2 - 225 - 25
22LEULEUVALVAL(chain B and (resseq 2:22 or resseq 24:27 or resseq...BB24 - 2627 - 29
23ALAALAARGARG(chain B and (resseq 2:22 or resseq 24:27 or resseq...BB29 - 3132 - 34
24VALVALVALVAL(chain B and (resseq 2:22 or resseq 24:27 or resseq...BB3336
25METMETILEILE(chain B and (resseq 2:22 or resseq 24:27 or resseq...BB36 - 6339 - 66
26PHEPHEGLNGLN(chain B and (resseq 2:22 or resseq 24:27 or resseq...BB65 - 10168 - 104
27THRTHRARGARG(chain B and (resseq 2:22 or resseq 24:27 or resseq...BB103 - 107106 - 110
28LEULEUTYRTYR(chain B and (resseq 2:22 or resseq 24:27 or resseq...BB109 - 129112 - 132
29ALAALAALAALA(chain B and (resseq 2:22 or resseq 24:27 or resseq...BB133136

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Components

#1: Protein Fatty acid-binding protein, heart / Fatty acid-binding protein 3 / Heart-type fatty acid-binding protein / H-FABP / Mammary-derived ...Fatty acid-binding protein 3 / Heart-type fatty acid-binding protein / H-FABP / Mammary-derived growth inhibitor / MDGI / Muscle fatty acid-binding protein / M-FABP


Mass: 15161.298 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP3, FABP11, MDGI / Production host: Escherichia coli (E. coli) / References: UniProt: P05413
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate, pH 7.0, 2.3 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 10, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.4→20.39 Å / Num. obs: 47516 / % possible obs: 96.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 10.974793779 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.033 / Net I/σ(I): 14
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 6777 / CC1/2: 0.895 / Rpim(I) all: 0.174 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HMS

1hms


Resolution: 1.40000091001→19.5420560352 Å / SU ML: 0.13276625966 / Cross valid method: FREE R-VALUE / σ(F): 1.33939847886 / Phase error: 18.0709695924
RfactorNum. reflection% reflection
Rfree0.197909732024 2364 4.97705166533 %
Rwork0.170195559929 --
obs0.171525378539 47498 96.3878404156 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.3235135462 Å2
Refinement stepCycle: LAST / Resolution: 1.40000091001→19.5420560352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 56 362 2526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005070734610572307
X-RAY DIFFRACTIONf_angle_d0.7806736961053115
X-RAY DIFFRACTIONf_chiral_restr0.0792924183924361
X-RAY DIFFRACTIONf_plane_restr0.00496432555509388
X-RAY DIFFRACTIONf_dihedral_angle_d14.4361804191867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.42860.2090896852331350.2048528930572577X-RAY DIFFRACTION94.297635605
1.4286-1.45960.2430255693611250.201891550572618X-RAY DIFFRACTION94.9134948097
1.4596-1.49360.232029041721540.1935861529172585X-RAY DIFFRACTION94.9064449064
1.4936-1.53090.239597664211560.1932249347182578X-RAY DIFFRACTION95.228143504
1.5309-1.57230.1940719317761380.1780823468042600X-RAY DIFFRACTION95.3342618384
1.5723-1.61850.2079483375531450.1835673314842636X-RAY DIFFRACTION95.8965517241
1.6185-1.67070.2067667716931240.1724314893812666X-RAY DIFFRACTION96.0743801653
1.6707-1.73040.2209273954881430.1720996290872631X-RAY DIFFRACTION96.0526315789
1.7304-1.79960.1850692871541340.169910006312638X-RAY DIFFRACTION96.5517241379
1.7996-1.88150.2082053959071450.1747056364422647X-RAY DIFFRACTION96.5088143795
1.8815-1.98060.2144361826731420.1707699355192668X-RAY DIFFRACTION97.23183391
1.9806-2.10460.2080419164571560.1747081326282663X-RAY DIFFRACTION97.3747841105
2.1046-2.26680.1665086951531210.1622054591312711X-RAY DIFFRACTION97.4200206398
2.2668-2.49450.2090172606911360.1723195690322717X-RAY DIFFRACTION98.1424148607
2.4945-2.85450.194075938911500.1771398122192706X-RAY DIFFRACTION98.0769230769
2.8545-3.59280.1699542204551380.1586745771012749X-RAY DIFFRACTION98.5324232082
3.5928-19.5440.1945330029371220.1563376180962744X-RAY DIFFRACTION96.077774053

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