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- PDB-6mp4: Human liver FABP1 bound to tetrahydrocannabinol -

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Basic information

Entry
Database: PDB / ID: 6mp4
TitleHuman liver FABP1 bound to tetrahydrocannabinol
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / Fatty Acid Binding Protein Cannabinoid
Function / homology
Function and homology information


cellular detoxification / Heme degradation / Triglyceride catabolism / antioxidant activity / peroxisomal matrix / fatty acid transport / Regulation of lipid metabolism by PPARalpha / fatty acid binding / PPARA activates gene expression / Cytoprotection by HMOX1 ...cellular detoxification / Heme degradation / Triglyceride catabolism / antioxidant activity / peroxisomal matrix / fatty acid transport / Regulation of lipid metabolism by PPARalpha / fatty acid binding / PPARA activates gene expression / Cytoprotection by HMOX1 / cellular response to hydrogen peroxide / cellular response to hypoxia / chromatin binding / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Lipocalin / cytosolic fatty-acid binding protein family / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
MALONATE ION / Chem-TCI / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsMcGoldrick, L.L. / Giuliano, C.J. / Elmes, M.W. / Deutsch, D.G. / Kaczocha, M. / Glynn, S.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)F31DA042545 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01DA035949 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01DA035923 United States
CitationJournal: Sci Rep / Year: 2019
Title: FABP1 controls hepatic transport and biotransformation of Delta 9 -THC.
Authors: Elmes, M.W. / Prentis, L.E. / McGoldrick, L.L. / Giuliano, C.J. / Sweeney, J.M. / Joseph, O.M. / Che, J. / Carbonetti, G.S. / Studholme, K. / Deutsch, D.G. / Rizzo, R.C. / Glynn, S.E. / Kaczocha, M.
History
DepositionOct 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid-binding protein, liver
B: Fatty acid-binding protein, liver
C: Fatty acid-binding protein, liver
D: Fatty acid-binding protein, liver
E: Fatty acid-binding protein, liver
F: Fatty acid-binding protein, liver
G: Fatty acid-binding protein, liver
H: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,53014
Polymers134,2818
Non-polymers1,2506
Water5,477304
1
A: Fatty acid-binding protein, liver
hetero molecules

F: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0895
Polymers33,5702
Non-polymers5193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area2810 Å2
ΔGint-2 kcal/mol
Surface area13420 Å2
MethodPISA
2
B: Fatty acid-binding protein, liver
E: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8853
Polymers33,5702
Non-polymers3141
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-9 kcal/mol
Surface area13690 Å2
MethodPISA
3
C: Fatty acid-binding protein, liver

G: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)33,5702
Polymers33,5702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area2200 Å2
ΔGint-10 kcal/mol
Surface area13810 Å2
MethodPISA
4
D: Fatty acid-binding protein, liver
hetero molecules

H: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9874
Polymers33,5702
Non-polymers4172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area2450 Å2
ΔGint-5 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.185, 79.291, 234.621
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -8 through 43 or resid 45...
21(chain B and (resid -8 through 43 or resid 45...
31(chain C and (resid -8 through 43 or resid 45...
41(chain D and (resid -8 through 43 or resid 45...
51(chain E and (resid -8 through 43 or resid 45...
61(chain F and (resid -8 through 43 or resid 45...
71(chain G and (resid -8 through 43 or resid 45...
81(chain H and (resid -8 through 43 or resid 45...

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
11GLYGLYGLNGLN(chain A and (resid -8 through 43 or resid 45...AA-8 - 4314 - 65
12GLYGLYLYSLYS(chain A and (resid -8 through 43 or resid 45...AA45 - 4667 - 68
13PHEPHELYSLYS(chain A and (resid -8 through 43 or resid 45...AA48 - 4970 - 71
14THRTHRGLUGLU(chain A and (resid -8 through 43 or resid 45...AA51 - 6873 - 90
15GLUGLUILEILE(chain A and (resid -8 through 43 or resid 45...AA70 - 12792 - 149
21GLYGLYGLNGLN(chain B and (resid -8 through 43 or resid 45...BB-8 - 4314 - 65
22GLYGLYLYSLYS(chain B and (resid -8 through 43 or resid 45...BB45 - 4667 - 68
23PHEPHELYSLYS(chain B and (resid -8 through 43 or resid 45...BB48 - 4970 - 71
24THRTHRGLUGLU(chain B and (resid -8 through 43 or resid 45...BB51 - 6873 - 90
25GLUGLUILEILE(chain B and (resid -8 through 43 or resid 45...BB70 - 12792 - 149
31GLYGLYGLNGLN(chain C and (resid -8 through 43 or resid 45...CC-8 - 4314 - 65
32GLYGLYLYSLYS(chain C and (resid -8 through 43 or resid 45...CC45 - 4667 - 68
33PHEPHELYSLYS(chain C and (resid -8 through 43 or resid 45...CC48 - 4970 - 71
34THRTHRGLUGLU(chain C and (resid -8 through 43 or resid 45...CC51 - 6873 - 90
35GLUGLUILEILE(chain C and (resid -8 through 43 or resid 45...CC70 - 12792 - 149
41GLYGLYGLNGLN(chain D and (resid -8 through 43 or resid 45...DD-8 - 4314 - 65
42GLYGLYLYSLYS(chain D and (resid -8 through 43 or resid 45...DD45 - 4667 - 68
43PHEPHELYSLYS(chain D and (resid -8 through 43 or resid 45...DD48 - 4970 - 71
44THRTHRGLUGLU(chain D and (resid -8 through 43 or resid 45...DD51 - 6873 - 90
45GLUGLUILEILE(chain D and (resid -8 through 43 or resid 45...DD70 - 12792 - 149
51GLYGLYGLNGLN(chain E and (resid -8 through 43 or resid 45...EE-8 - 4314 - 65
52GLYGLYLYSLYS(chain E and (resid -8 through 43 or resid 45...EE45 - 4667 - 68
53PHEPHELYSLYS(chain E and (resid -8 through 43 or resid 45...EE48 - 4970 - 71
54THRTHRGLUGLU(chain E and (resid -8 through 43 or resid 45...EE51 - 6873 - 90
55GLUGLUILEILE(chain E and (resid -8 through 43 or resid 45...EE70 - 12792 - 149
61GLYGLYGLNGLN(chain F and (resid -8 through 43 or resid 45...FF-8 - 4314 - 65
62GLYGLYLYSLYS(chain F and (resid -8 through 43 or resid 45...FF45 - 4667 - 68
63PHEPHELYSLYS(chain F and (resid -8 through 43 or resid 45...FF48 - 4970 - 71
64THRTHRGLUGLU(chain F and (resid -8 through 43 or resid 45...FF51 - 6873 - 90
65GLUGLUILEILE(chain F and (resid -8 through 43 or resid 45...FF70 - 12792 - 149
71GLYGLYGLNGLN(chain G and (resid -8 through 43 or resid 45...GG-8 - 4314 - 65
72GLYGLYLYSLYS(chain G and (resid -8 through 43 or resid 45...GG45 - 4667 - 68
73PHEPHELYSLYS(chain G and (resid -8 through 43 or resid 45...GG48 - 4970 - 71
74THRTHRGLUGLU(chain G and (resid -8 through 43 or resid 45...GG51 - 6873 - 90
75GLUGLUILEILE(chain G and (resid -8 through 43 or resid 45...GG70 - 12792 - 149
81GLYGLYGLNGLN(chain H and (resid -8 through 43 or resid 45...HH-8 - 4314 - 65
82GLYGLYLYSLYS(chain H and (resid -8 through 43 or resid 45...HH45 - 4667 - 68
83PHEPHELYSLYS(chain H and (resid -8 through 43 or resid 45...HH48 - 4970 - 71
84THRTHRGLUGLU(chain H and (resid -8 through 43 or resid 45...HH51 - 6873 - 90
85GLUGLUILEILE(chain H and (resid -8 through 43 or resid 45...HH70 - 12792 - 149

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Components

#1: Protein
Fatty acid-binding protein, liver / Fatty acid-binding protein 1 / Liver-type fatty acid-binding protein / L-FABP


Mass: 16785.117 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP1, FABPL / Production host: Escherichia coli (E. coli) / References: UniProt: P07148
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-TCI / (6aR,10aR)-6,6,9-trimethyl-3-pentyl-6a,7,8,10a-tetrahydro-6H-benzo[c]chromen-1-ol / Tetrahydrocannabinol


Mass: 314.462 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 3 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 1.4 M sodium malonate 0.1 M Bis Tris HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.1808 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.49
ReflectionResolution: 2.5→40.515 Å / Num. obs: 51960 / % possible obs: 100 % / Redundancy: 8.1 % / Net I/σ(I): 26.7
Reflection shellResolution: 2.5→2.54 Å / Mean I/σ(I) obs: 1.91

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2STM

2stm


Resolution: 2.502→40.515 Å / Cross valid method: THROUGHOUT / σ(F): 100.63 / Phase error: 25.77 / Details: Refined with twin law k,h,-l
RfactorNum. reflection% reflection
Rfree0.2245 2649 5.11 %
Rwork0.2058 --
obs0.2095 51884 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.94 Å2 / Biso mean: 66.2108 Å2 / Biso min: 16.46 Å2
Refinement stepCycle: final / Resolution: 2.502→40.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8562 0 90 304 8956
Biso mean--70.06 45.9 -
Num. residues----1089
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5178X-RAY DIFFRACTION5.272TORSIONAL
12B5178X-RAY DIFFRACTION5.272TORSIONAL
13C5178X-RAY DIFFRACTION5.272TORSIONAL
14D5178X-RAY DIFFRACTION5.272TORSIONAL
15E5178X-RAY DIFFRACTION5.272TORSIONAL
16F5178X-RAY DIFFRACTION5.272TORSIONAL
17G5178X-RAY DIFFRACTION5.272TORSIONAL
18H5178X-RAY DIFFRACTION5.272TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5038-2.54940.2991400.28992589272995
2.5494-2.59840.30141450.30552499264495
2.5984-2.65140.28681330.29622554268795
2.6514-2.7090.2651170.30992552266996
2.709-2.7720.32081300.28912568269895
2.772-2.84120.3151230.28982565268895
2.8412-2.9180.30911370.2892572270995
2.918-3.00380.32431390.28022552269195
3.0038-3.10070.24371370.26712564270195
3.1007-3.21140.28841510.24632579273094
3.2114-3.33980.23221340.22972558269295
3.3398-3.49160.24311450.22522557270295
3.4916-3.67540.22311490.20872575272495
3.6754-3.90530.24591360.20252570270695
3.9053-4.20610.20191590.1822605276494
4.2061-4.62820.16221280.15532619274795
4.6282-5.29490.18391500.14412633278395
5.2949-6.660.1851320.17992663279595
6.66-30.87470.21721630.19172772293594
Refinement TLS params.Method: refined / Origin x: 4.3851 Å / Origin y: -23.8551 Å / Origin z: -28.0574 Å
111213212223313233
T0.8414 Å20.0592 Å2-0.0315 Å2-0.7205 Å2-0.0048 Å2--0.2446 Å2
L0.0315 °20.0386 °2-0.0315 °2-0.2899 °2-0.0899 °2--0.4464 °2
S-0.0621 Å °-0.0667 Å °0.0324 Å °0.0371 Å °-0.0311 Å °-0.0149 Å °-0.1829 Å °0.0063 Å °0.0949 Å °
Refinement TLS groupSelection details: chain a or chain b or chain c or chain d or chain e or chain f or chain g or chain h or chain j or chain k

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