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- PDB-2vya: Crystal Structure of fatty acid amide hydrolase conjugated with t... -

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Basic information

Entry
Database: PDB / ID: 2vya
TitleCrystal Structure of fatty acid amide hydrolase conjugated with the drug-like inhibitor PF-750
ComponentsFATTY-ACID AMIDE HYDROLASE 1
KeywordsHYDROLASE / FATTY ACID AMIDE HYDROLYSE / GOLGI APPARATUS / ENDOPLASMIC RETICULUM / INHIBITOR / DRUG- LIKE / TRANSMEMBRANE / FAAH / CHIMERA / MEMBRANE / COVALENT / HUMANIZED
Function / homology
Function and homology information


Arachidonate metabolism / fatty acid amide hydrolase / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / fatty acid amide hydrolase activity / monoacylglycerol catabolic process / monoacylglycerol lipase activity / amidase activity / fatty acid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity, acting on ester bonds ...Arachidonate metabolism / fatty acid amide hydrolase / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / fatty acid amide hydrolase activity / monoacylglycerol catabolic process / monoacylglycerol lipase activity / amidase activity / fatty acid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity, acting on ester bonds / organelle membrane / positive regulation of vasoconstriction / fatty acid metabolic process / phospholipid binding / presynapse / postsynapse / Golgi membrane / lipid binding / glutamatergic synapse / endoplasmic reticulum membrane / identical protein binding
Similarity search - Function
: / Amidase, conserved site / Amidases signature. / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-PF7 / Fatty-acid amide hydrolase 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMileni, M. / Johnson, D.S. / Wang, Z. / Everdeen, D.S. / Liimatta, M. / Pabst, B. / Bhattacharya, K. / Nugent, R.A. / Kamtekar, S. / Cravatt, B.F. ...Mileni, M. / Johnson, D.S. / Wang, Z. / Everdeen, D.S. / Liimatta, M. / Pabst, B. / Bhattacharya, K. / Nugent, R.A. / Kamtekar, S. / Cravatt, B.F. / Ahn, K. / Stevens, R.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structure-Guided Inhibitor Design for Human Faah by Interspecies Active Site Conversion.
Authors: Mileni, M. / Johnson, D.S. / Wang, Z. / Everdeen, D.S. / Liimatta, M. / Pabst, B. / Bhattacharya, K. / Nugent, R.A. / Kamtekar, S. / Cravatt, B.F. / Ahn, K. / Stevens, R.C.
History
DepositionJul 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FATTY-ACID AMIDE HYDROLASE 1
B: FATTY-ACID AMIDE HYDROLASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,0179
Polymers129,4402
Non-polymers5767
Water1,51384
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-23.5 kcal/mol
Surface area45720 Å2
MethodPQS
Unit cell
Length a, b, c (Å)103.690, 103.690, 253.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein FATTY-ACID AMIDE HYDROLASE 1 / FATTY ACID AMIDE HYDROLASE / OLEAMIDE HYDROLASE 1 / ANANDAMIDE AMIDOHYDROLASE 1


Mass: 64720.234 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-579 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: S241 IS CARBAMYLATED TO 4-(QUINOLIN-3-YLMETHYL)PIPERIDINE-1-CARBALDEHYDE CHEMICAL FORMULA, C16H18N2O
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): A.I. / References: UniProt: P97612, amidase
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical ChemComp-PF7 / 4-(quinolin-3-ylmethyl)piperidine-1-carboxylic acid


Mass: 270.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18N2O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 192 TO PHE ENGINEERED RESIDUE IN CHAIN A, PHE 194 TO TYR ...ENGINEERED RESIDUE IN CHAIN A, LEU 192 TO PHE ENGINEERED RESIDUE IN CHAIN A, PHE 194 TO TYR ENGINEERED RESIDUE IN CHAIN A, ALA 377 TO THR ENGINEERED RESIDUE IN CHAIN A, SER 435 TO ASN ENGINEERED RESIDUE IN CHAIN A, ILE 491 TO VAL ENGINEERED RESIDUE IN CHAIN A, VAL 495 TO MET ENGINEERED RESIDUE IN CHAIN B, LEU 192 TO PHE ENGINEERED RESIDUE IN CHAIN B, PHE 194 TO TYR ENGINEERED RESIDUE IN CHAIN B, ALA 377 TO THR ENGINEERED RESIDUE IN CHAIN B, SER 435 TO ASN ENGINEERED RESIDUE IN CHAIN B, ILE 491 TO VAL ENGINEERED RESIDUE IN CHAIN B, VAL 495 TO MET
Nonpolymer details4--QUINOLIN-3-YLMETHYL--PIPERIDINE-1-CARBALDEHYDE (PF7): CARBAMYLATED TO SERINE 241

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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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 5.5 / Details: PEG 400 10% NACL 100MM MES 100MM PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.75→40 Å / Num. obs: 40178 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 7
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.1 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MT5

1mt5


Resolution: 2.75→38.26 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.899 / SU B: 25.859 / SU ML: 0.233 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.759 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES MARKED UNX REPRESENT UNEXPLAINED DENSITY WITHIN THE ACTIVE SITE. THEY ARE INCLUDED HERE AS THEY MAY REPRESENT IMPORTANT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES MARKED UNX REPRESENT UNEXPLAINED DENSITY WITHIN THE ACTIVE SITE. THEY ARE INCLUDED HERE AS THEY MAY REPRESENT IMPORTANT INFORMATION THAT WILL BE USEFUL IN FUTURE STUDIES. THESE ATOMS HAVE BEEN GIVEN 0.00 OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2014 5 %RANDOM
Rwork0.188 ---
obs0.191 38162 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.79 Å2
Baniso -1Baniso -2Baniso -3
1-2.53 Å21.27 Å20 Å2
2--2.53 Å20 Å2
3----3.8 Å2
Refinement stepCycle: LAST / Resolution: 2.75→38.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8365 0 43 84 8492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228599
X-RAY DIFFRACTIONr_bond_other_d0.0020.025967
X-RAY DIFFRACTIONr_angle_refined_deg1.5852.01211665
X-RAY DIFFRACTIONr_angle_other_deg0.928314580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9751082
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.66723.819343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.637151468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8471556
X-RAY DIFFRACTIONr_chiral_restr0.0750.21305
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029504
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021680
X-RAY DIFFRACTIONr_nbd_refined0.2160.22200
X-RAY DIFFRACTIONr_nbd_other0.190.26360
X-RAY DIFFRACTIONr_nbtor_refined0.1840.24261
X-RAY DIFFRACTIONr_nbtor_other0.0910.24593
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4891.56974
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.628703
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.03233721
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6084.52958
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.335 147
Rwork0.285 2840
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)
113.4786-5.9393-1.22294.86760.24293.77060.38721.43350.3998-0.7891-0.3129-0.1462-0.2570.1478-0.07430.3874-0.17130.07110.14780.0611-0.098664.2633-4.9171-56.4892
24.0747-0.78541.53073.13410.15083.3731-0.33970.27480.1876-0.4740.2783-0.7124-0.3230.69530.06140.1003-0.14830.17310.2040.00690.068275.0623-11.6661-46.9107
32.1408-0.2681.11250.83350.28141.46-0.130.25290.1545-0.3350.1049-0.0841-0.1080.15880.0250.0523-0.1080.0689-0.05180.0014-0.141358.5375-10.7141-39.7982
40.5912-0.19450.37692.1762-1.04460.64150.02960.1556-0.11890.0648-0.0468-0.45460.21760.29610.01710.0053-0.0470.1245-0.06-0.119-0.03666.8437-21.408-26.1344
51.2203-0.25680.11781.30540.26161.5714-0.07630.1396-0.0775-0.1308-0.00090.13460.1995-0.16640.0772-0.0383-0.11040.0289-0.1092-0.0394-0.107246.1889-23.8969-32.0775
67.01330.32291.8961.8193-0.28164.0516-0.1799-0.90930.1280.29690.13760.11620.133-0.40250.04230.1579-0.13330.0555-0.1027-0.0453-0.108951.3327-15.569721.7745
75.5468-0.6878-1.05262.81850.62273.20910.0288-0.2273-0.4130.2846-0.0802-0.30520.59560.14590.05140.1336-0.0118-0.0421-0.05950.0641-0.114165.386-17.49315.0838
81.0854-0.101-0.04150.5116-0.2921.32610.059-0.0580.00660.0575-0.06240.00560.1044-0.02410.0034-0.0735-0.08250.0327-0.1439-0.0315-0.112253.746-8.56224.6566
91.9880.54390.25280.9310.26931.3004-0.01040.0151-0.09620.04730.1268-0.50960.05090.376-0.1164-0.0884-0.08890.007-0.069-0.0641-0.13869.5872-6.2151-6.0371
100.71870.24410.09821.57050.32841.44970.00430.06980.1206-0.1256-0.01770.1284-0.2442-0.05860.0134-0.0875-0.06840.0065-0.1851-0.0216-0.102953.96228.8396-4.5017
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 75
2X-RAY DIFFRACTION2A76 - 134
3X-RAY DIFFRACTION3A135 - 284
4X-RAY DIFFRACTION4A285 - 335
5X-RAY DIFFRACTION5A336 - 575
6X-RAY DIFFRACTION6B34 - 75
7X-RAY DIFFRACTION7B76 - 134
8X-RAY DIFFRACTION8B135 - 284
9X-RAY DIFFRACTION9B285 - 335
10X-RAY DIFFRACTION10B336 - 574

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