[English] 日本語
Yorodumi
- PDB-2wap: 3D-crystal structure of humanized-rat fatty acid amide hydrolase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wap
Title3D-crystal structure of humanized-rat fatty acid amide hydrolase (FAAH) conjugated with the drug-like urea inhibitor PF-3845
ComponentsFATTY-ACID AMIDE HYDROLASE 1
KeywordsHYDROLASE / FATTY ACID AMIDE HYDROLASE / UREA INHIBITOR / GOLGI APPARATUS / ENDOPLASMIC RETICULUM / ACYL- ENZYME / TRANSMEMBRANE / PHOSPHOPROTEIN / FAAH / DRUG / MEMBRANE / INHIBITOR
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 / endoplasmic reticulum membrane / glutamatergic synapse / 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-PIX / Fatty-acid amide hydrolase 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMileni, M. / Kamtekar, S. / Stevens, R.C.
CitationJournal: Chem.Biol. / Year: 2009
Title: Discovery and Characterization of a Highly Selective Faah Inhibitor that Reduces Inflammatory Pain.
Authors: Ahn, K. / Johnson, D.S. / Mileni, M. / Beidler, D. / Long, J.Z. / Mckinney, M.K. / Weerapana, E. / Sadagopan, N. / Liimatta, M. / Smith, S.E. / Lazerwith, S. / Stiff, C. / Kamtekar, S. / ...Authors: Ahn, K. / Johnson, D.S. / Mileni, M. / Beidler, D. / Long, J.Z. / Mckinney, M.K. / Weerapana, E. / Sadagopan, N. / Liimatta, M. / Smith, S.E. / Lazerwith, S. / Stiff, C. / Kamtekar, S. / Bhattacharya, K. / Zhang, Y. / Swaney, S. / Vanbecelaere, K. / Stevens, R.C. / Cravatt, B.F.
History
DepositionFeb 11, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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_ncs_dom_lim / 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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)120,5198
Polymers119,6542
Non-polymers8656
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-62.16 kcal/mol
Surface area35830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.770, 105.200, 148.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLEULEUAA33 - 1343 - 104
21GLYGLYLEULEUBB33 - 1343 - 104
12TYRTYRCYSCYSAA135 - 299105 - 269
22TYRTYRCYSCYSBB135 - 299105 - 269
13GLUGLUGLUGLUAA300 - 331270 - 301
23GLUGLUGLUGLUBB300 - 331270 - 301
14THRTHRLEULEUAA332 - 447302 - 417
24THRTHRLEULEUBB332 - 447302 - 417
15GLNGLNTHRTHRAA448 - 573418 - 543
25GLNGLNTHRTHRBB448 - 573418 - 543

NCS ensembles :
ID
1
2
3
4
5

-
Components

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


Mass: 59827.020 Da / Num. of mol.: 2 / Fragment: RESIDUES 31-573 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: S241 IS CARBAMYLATED TO\: 4-(3-(5-(TRIFLUOROMETHYL)PYRIDIN-2-YLOXY)BENZYL)PIPERIDINE-1-CARBALDEHYDE
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Description: HUMANIZED ACTIVE SITE (6 MUTATIONS) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 AI / References: UniProt: P97612, amidase
#2: Chemical ChemComp-PIX / 4-(3-{[5-(trifluoromethyl)pyridin-2-yl]oxy}benzyl)piperidine-1-carboxylic acid


Mass: 380.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19F3N2O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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
Has protein modificationY
Sequence detailsTHE 6 MUTATIONS INTRODUCED INTO THE SEQUENCES WERE DONE SO WITH THE AIM OF MAKING THE ACTIVE SITE ...THE 6 MUTATIONS INTRODUCED INTO THE SEQUENCES WERE DONE SO WITH THE AIM OF MAKING THE ACTIVE SITE MORE LIKE THE HUMAN EQUIVALENT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growpH: 6.5 / Details: NACL 100MM, PEG4000 12%, MES 100MM PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 37781 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VYA

2vya


Resolution: 2.8→37.01 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / SU B: 25.64 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.807 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1963 4.9 %RANDOM
Rwork0.192 ---
obs0.194 37799 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.09 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2--0.12 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.8→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8369 0 56 43 8468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228615
X-RAY DIFFRACTIONr_bond_other_d0.0020.027970
X-RAY DIFFRACTIONr_angle_refined_deg1.5812.01311695
X-RAY DIFFRACTIONr_angle_other_deg0.846318582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98551082
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.92423.79343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.214151468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1441556
X-RAY DIFFRACTIONr_chiral_restr0.0780.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021689
X-RAY DIFFRACTIONr_nbd_refined0.210.22198
X-RAY DIFFRACTIONr_nbd_other0.1870.28612
X-RAY DIFFRACTIONr_nbtor_refined0.1830.24332
X-RAY DIFFRACTIONr_nbtor_other0.0930.24873
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2253
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2381.55402
X-RAY DIFFRACTIONr_mcbond_other0.0511.52190
X-RAY DIFFRACTIONr_mcangle_it0.49628699
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.92933314
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5814.52990
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A601tight positional0.030.05
21A954tight positional0.030.05
22B954tight positional0.030.05
31A186tight positional0.040.05
32B186tight positional0.040.05
41A679tight positional0.040.05
42B679tight positional0.040.05
51A742tight positional00.05
52B742tight positional00.05
11A950medium positional0.670.5
21A1323medium positional0.370.5
22B1323medium positional0.370.5
31A345medium positional0.340.5
32B345medium positional0.340.5
41A1166medium positional0.440.5
42B1166medium positional0.440.5
51A1184medium positional00.5
52B1184medium positional00.5
11A601tight thermal0.040.5
21A954tight thermal0.050.5
22B954tight thermal0.050.5
31A186tight thermal0.050.5
32B186tight thermal0.050.5
41A679tight thermal0.050.5
42B679tight thermal0.050.5
51A742tight thermal00.5
52B742tight thermal00.5
11A950medium thermal0.232
21A1323medium thermal0.262
22B1323medium thermal0.262
31A345medium thermal0.22
32B345medium thermal0.22
41A1166medium thermal0.282
42B1166medium thermal0.282
51A1184medium thermal02
52B1184medium thermal02
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 122 -
Rwork0.3 2769 -
obs--99.48 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more