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- PDB-7fwi: Crystal Structure of human FABP5 in complex with 2-(indole-1-carb... -

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Basic information

Entry
Database: PDB / ID: 7fwi
TitleCrystal Structure of human FABP5 in complex with 2-(indole-1-carbonylamino)benzoic acid
ComponentsFatty acid-binding protein 5
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING
Function / homology
Function and homology information


regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Signaling by Retinoic Acid / long-chain fatty acid transmembrane transporter activity ...regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Signaling by Retinoic Acid / long-chain fatty acid transmembrane transporter activity / Triglyceride catabolism / epidermis development / fatty acid transport / long-chain fatty acid transport / secretory granule membrane / fatty acid binding / lipid metabolic process / glucose metabolic process / azurophil granule lumen / glucose homeostasis / positive regulation of cold-induced thermogenesis / postsynaptic density / lipid binding / synapse / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin
Similarity search - Domain/homology
Chem-NC0 / Fatty acid-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Ning, R. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: To be published
Title: Crystal Structure of a human FABP5 complex
Authors: Obst, U. / Magnone, C. / Kuhn, B. / Rudolph, M.G.
History
DepositionApr 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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 5
B: Fatty acid-binding protein 5
C: Fatty acid-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0748
Polymers46,4033
Non-polymers6715
Water82946
1
A: Fatty acid-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7853
Polymers15,4681
Non-polymers3182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5032
Polymers15,4681
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fatty acid-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7853
Polymers15,4681
Non-polymers3182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.431, 38.443, 80.320
Angle α, β, γ (deg.)90.000, 100.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fatty acid-binding protein 5 / Epidermal-type fatty acid-binding protein / E-FABP / Fatty acid-binding protein / epidermal / ...Epidermal-type fatty acid-binding protein / E-FABP / Fatty acid-binding protein / epidermal / Psoriasis-associated fatty acid-binding protein homolog / PA-FABP


Mass: 15467.732 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP5 / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01469
#2: Chemical ChemComp-NC0 / 2-[(2,3-dihydro-1H-indole-1-carbonyl)amino]benzoic acid


Mass: 282.294 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.78 Å3/Da / Density % sol: 30.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→40.93 Å / Num. obs: 22364 / % possible obs: 98 % / Redundancy: 3.29 % / Biso Wilson estimate: 27.91 Å2 / Rmerge(I) obs: 0.161 / Net I/σ(I): 4.69 / Num. measured all: 131660
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. possibleNum. unique obsNet I/σ(I) obs% possible all
1.99-2.043.390.781132612861.0697
2.04-2.083.380.754120611781.1597.7
2.08-2.133.330.683137213321.3497.1
2.13-2.183.280.66126912381.4597.6
2.18-2.233.120.576116111371.7397.9
2.23-2.293.20.557125112161.9697.2
2.29-2.363.40.54129312592.2397.4
2.36-2.433.430.499116011332.497.7
2.43-2.513.340.469116511382.6597.7
2.51-2.63.30.387117111463.1897.9
2.6-2.713.290.333119211743.5698.5
2.71-2.843.130.269118911704.2298.4
2.84-2.993.170.217114511285.1198.5
2.99-3.183.450.178116811546.8398.8
3.18-3.443.370.124117511568.3698.4
3.44-3.83.330.096116311519.7699
3.8-4.363.010.0821133112010.2598.9
4.36-5.513.40.0671143112812.0598.7
5.51-40.933.090.0581148112011.8497.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2→39.47 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.75 / Stereochemistry target values: ML
Details: 3 molecules per a.u., one of which is apo chloride ion in binding site
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1123 5.1 %RANDOM
Rwork0.227 20887 --
obs0.2295 22010 97.9 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.39 Å2 / Biso mean: 34.1556 Å2 / Biso min: 12.43 Å2
Refinement stepCycle: final / Resolution: 2→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 0 45 46 3235
Biso mean--31.77 31.79 -
Num. residues----403
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.090.35221370.31272575271297
2.09-2.20.35531250.3022560268598
2.2-2.340.32891210.28942598271997
2.34-2.520.35391510.29622572272398
2.52-2.770.34031570.26932612276998
2.77-3.170.25941380.23262619275798
3.17-40.23741540.18552626278099
4-39.470.22061400.18132725286598
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.90612.42742.28073.092.9412.82470.49490.17240.79120.0712-1.0576-0.82560.01040.0889-0.3440.31140.0517-0.00420.22630.13560.43543.41269.58710.9572
20.0767-0.0781-0.41280.2512-0.44110.3155-0.25860.4931-0.20080.0674-0.07290.07340.3421-0.1787-0.00470.2187-0.0063-0.00940.23320.01480.2065-5.8212-4.66775.0123
30.15280.18410.05911.0453-0.10620.5064-0.280.0511-0.2493-0.2084-0.0030.47540.044-0.1948-0.00780.17930.0142-0.02850.1962-0.02850.2827-2.6526-20.571411.9043
41.4954-0.5111-0.61330.79070.01460.30390.2064-0.2778-0.24670.0227-0.1261-0.3265-0.0428-0.44920.00560.18790.0089-0.00450.21260.0260.1311-5.70990.517916.1346
50.7550.4402-0.0182-0.10050.35240.60380.0146-0.04710.08720.0784-0.00380.00510.0338-0.07090.00010.2807-0.0026-0.00330.20060.00070.22990.6486-5.21122.6104
60.27070.2422-0.63661.4598-0.44870.7757-0.4815-0.33630.2483-0.3473-0.0701-1.3691-0.17540.363-0.10070.2968-0.0677-0.08350.18070.09320.29578.248-5.427218.164
71.23790.1316-0.55420.89870.80280.99760.01760.0561-0.2054-0.1890.03540.03930.12950.09520.00080.13720.00920.00690.16910.02750.15385.6313-6.764611.146
81.8182-0.30520.07980.3021-0.06640.0386-0.335-0.3159-0.5310.39320.55260.3144-0.2765-0.1550.05290.20290.0321-0.05390.17350.0450.14771.02-8.33836.9315
91.23820.75240.25820.38020.49970.87790.1690.1355-0.57450.2454-0.25-0.2505-0.1044-0.01910.00190.18670.0004-0.01170.18370.02410.2826.8273-4.46816.502
100.45120.41110.5441.00790.11250.36270.0279-0.15860.14370.0711-0.0396-0.1016-0.04570.1355-0.00010.1825-0.02190.04280.24890.02660.308429.916617.447712.8011
11-0.11950.1145-0.39851.26751.01070.87970.0341-0.0507-0.61950.30460.051-0.25550.05970.31970.15030.2170.0532-0.05830.25710.07030.317831.112-3.42214.3375
121.2198-1.5091-0.43071.91810.51580.8177-0.389-0.1691-0.42220.53360.16450.0637-0.0560.1090.00020.34240.02720.04880.33160.06110.29524.74781.533420.6963
130.51380.5732-0.11121.57990.2674-0.127-0.0193-0.18080.23840.21690.08590.2336-0.01410.114-0.00010.2080.0512-0.00860.18110.01310.297920.04775.273212.7035
140.8737-0.7644-0.57840.36240.7150.16260.2980.05631.07650.20370.1803-0.4474-0.1337-0.05350.04420.19810.01630.00910.1899-0.01550.37825.75636.5646.3406
152.37030.6361-0.82171.3014-0.16870.63360.11520.25511.4342-0.05650.14460.6635-0.269-0.0980.20890.280.0205-0.060.2761-0.01880.26662.660815.238444.1173
160.02440.1954-0.01770.1432-0.1040.39670.1478-0.0487-0.2291-0.205-0.0275-0.12870.292-0.2610.00020.3037-0.02570.05110.2603-0.0030.247-2.1485-5.942449.5242
170.59480.1323-0.81490.6336-0.87791.2167-0.0143-0.01540.0210.03280.0749-0.0915-0.11530.126200.23250.00210.00090.3534-0.01270.239610.79196.419946.4012
180.82390.1017-0.71831.33930.90520.9670.12920.1585-0.0549-0.3051-0.17760.04360.36060.23200.23150.04260.0140.26140.00340.289510.13622.629435.6494
191.11460.77670.73010.55480.00031.1959-0.14610.1864-0.01340.00330.13080.24190.0283-0.01080.00010.19870.02010.03680.20180.01140.14611.81094.897238.3223
200.95360.1823-0.41690.1731-0.09430.4563-0.20960.09690.0067-0.18630.2091-0.2525-0.024-0.118-0.00240.2063-0.0162-0.00990.1747-0.02910.1586-2.39276.292543.0645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 8 )A1 - 8
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 17 )A9 - 17
3X-RAY DIFFRACTION3chain 'A' and (resid 18 through 38 )A18 - 38
4X-RAY DIFFRACTION4chain 'A' and (resid 39 through 58 )A39 - 58
5X-RAY DIFFRACTION5chain 'A' and (resid 59 through 90 )A59 - 90
6X-RAY DIFFRACTION6chain 'A' and (resid 91 through 100 )A91 - 100
7X-RAY DIFFRACTION7chain 'A' and (resid 101 through 122 )A101 - 122
8X-RAY DIFFRACTION8chain 'A' and (resid 123 through 134 )A123 - 134
9X-RAY DIFFRACTION9chain 'B' and (resid -1 through 17 )B-1 - 17
10X-RAY DIFFRACTION10chain 'B' and (resid 18 through 38 )B18 - 38
11X-RAY DIFFRACTION11chain 'B' and (resid 39 through 58 )B39 - 58
12X-RAY DIFFRACTION12chain 'B' and (resid 59 through 93 )B59 - 93
13X-RAY DIFFRACTION13chain 'B' and (resid 94 through 122 )B94 - 122
14X-RAY DIFFRACTION14chain 'B' and (resid 123 through 134 )B123 - 134
15X-RAY DIFFRACTION15chain 'C' and (resid 2 through 17 )C2 - 17
16X-RAY DIFFRACTION16chain 'C' and (resid 18 through 36 )C18 - 36
17X-RAY DIFFRACTION17chain 'C' and (resid 37 through 81 )C37 - 81
18X-RAY DIFFRACTION18chain 'C' and (resid 82 through 100 )C82 - 100
19X-RAY DIFFRACTION19chain 'C' and (resid 101 through 122 )C101 - 122
20X-RAY DIFFRACTION20chain 'C' and (resid 123 through 134 )C123 - 134

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