[English] 日本語
Yorodumi
- PDB-3znp: IN VITRO AND IN VIVO INHIBITION OF HUMAN D-AMINO ACID OXIDASE: RE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3znp
TitleIN VITRO AND IN VIVO INHIBITION OF HUMAN D-AMINO ACID OXIDASE: REGULATION OF D-SERINE CONCENTRATION IN THE BRAIN
ComponentsD-AMINO-ACID OXIDASE
KeywordsOXIDOREDUCTASE / SMALL MOLECULE INHIBITION / NEUROTRANSMISSION
Function / homology
Function and homology information


D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / D-serine metabolic process / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process / presynaptic active zone ...D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / D-serine metabolic process / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process / presynaptic active zone / neutrophil-mediated killing of gram-negative bacterium / peroxisomal matrix / digestion / FAD binding / Peroxisomal protein import / identical protein binding / cytoplasm / cytosol
Similarity search - Function
D-amino acid oxidase, conserved site / D-amino-acid oxidase / D-amino acid oxidases signature. / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich ...D-amino acid oxidase, conserved site / D-amino-acid oxidase / D-amino acid oxidases signature. / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 3-HYDROXY-2H-CHROMEN-2-ONE / D-amino-acid oxidase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHopkins, S.C. / Heffernan, M.L.R. / Saraswat, L.D. / Bowen, C.A. / Melnick, L. / Hardy, L.W. / Orsini, M.A. / Allen, M.S. / Koch, P. / Spear, K.L. ...Hopkins, S.C. / Heffernan, M.L.R. / Saraswat, L.D. / Bowen, C.A. / Melnick, L. / Hardy, L.W. / Orsini, M.A. / Allen, M.S. / Koch, P. / Spear, K.L. / Foglesong, R.J. / Soukri, M. / Chytil, M. / Fang, Q.K. / Jones, S.W. / Varney, M.A. / Panatier, A. / Oliet, S.H.R. / Pollegioni, L. / Piubelli, L. / Molla, G. / Nardini, M. / Large, T.H.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Structural, Kinetic, and Pharmacodynamic Mechanisms of D-Amino Acid Oxidase Inhibition by Small Molecules.
Authors: Hopkins, S.C. / Heffernan, M.L.R. / Saraswat, L.D. / Bowen, C.A. / Melnick, L. / Hardy, L.W. / Orsini, M.A. / Allen, M.S. / Koch, P. / Spear, K.L. / Foglesong, R.J. / Soukri, M. / Chytil, M. ...Authors: Hopkins, S.C. / Heffernan, M.L.R. / Saraswat, L.D. / Bowen, C.A. / Melnick, L. / Hardy, L.W. / Orsini, M.A. / Allen, M.S. / Koch, P. / Spear, K.L. / Foglesong, R.J. / Soukri, M. / Chytil, M. / Fang, Q.K. / Jones, S.W. / Varney, M.A. / Panatier, A. / Oliet, S.H.R. / Pollegioni, L. / Piubelli, L. / Molla, G. / Nardini, M. / Large, T.H.
History
DepositionFeb 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Dec 20, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-AMINO-ACID OXIDASE
B: D-AMINO-ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,42012
Polymers79,0422
Non-polymers2,37810
Water1,78399
1
A: D-AMINO-ACID OXIDASE
hetero molecules

A: D-AMINO-ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,67414
Polymers79,0422
Non-polymers2,63212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area7390 Å2
ΔGint-37.5 kcal/mol
Surface area27560 Å2
MethodPISA
2
B: D-AMINO-ACID OXIDASE
hetero molecules

B: D-AMINO-ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,16510
Polymers79,0422
Non-polymers2,1248
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area6940 Å2
ΔGint-33.1 kcal/mol
Surface area28060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.069, 84.069, 189.163
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein D-AMINO-ACID OXIDASE / DAAO / DAMOX / DAO / D-AMINO ACID OXIDASE


Mass: 39520.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14920, D-amino-acid oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SE2 / 3-HYDROXY-2H-CHROMEN-2-ONE


Mass: 162.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.62 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Type: ALS / Wavelength: 1.24
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.4→47.66 Å / Num. obs: 30588 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3.27 % / Biso Wilson estimate: 67.89 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.27 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.9 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
d*TREKdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DU8

2du8


Resolution: 2.4→34.98 Å / Cor.coef. Fo:Fc: 0.9329 / Cor.coef. Fo:Fc free: 0.8818 / SU R Cruickshank DPI: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.503 / SU Rfree Blow DPI: 0.318 / SU Rfree Cruickshank DPI: 0.323
Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. POOR DENSITY IS PRESENT FOR RESIDUES A28, A29, A30, A31, A297, A298, A299, A300, A301, A302, A303, A335, A336, A337, A338, A339, A340, B24, ...Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. POOR DENSITY IS PRESENT FOR RESIDUES A28, A29, A30, A31, A297, A298, A299, A300, A301, A302, A303, A335, A336, A337, A338, A339, A340, B24, B25, B26, B27, B28, B29, B30, B31, B32, B55, B56, B57, B58, B59, B60, B61, B62, B85, B117, B123, B128, B129, B166, B167, B168, B188, B189, B190, B191, B192, B193, B194, B195, B196, B220, B221, B222, B223, B224, B253, B254, B255, B256, B260, B261, B295, B296, B297, B298, B299, B300, B301, B302, B303, B335, B336, B337, B338, B339, B340. FINAL STRUCTURE HAS NO RESIDUES IN THE DISALLOWED REGION OF THE RAMACHANDRAN PLOT AS DEFINED IN THE CCP4 PROCHECK PROGRAM.
RfactorNum. reflection% reflectionSelection details
Rfree0.3067 1539 5.04 %RANDOM
Rwork0.2318 ---
obs0.2356 30523 98.23 %-
Displacement parametersBiso mean: 88.17 Å2
Baniso -1Baniso -2Baniso -3
1-2.6684 Å20 Å20 Å2
2--2.6684 Å20 Å2
3----5.3367 Å2
Refine analyzeLuzzati coordinate error obs: 0.582 Å
Refinement stepCycle: LAST / Resolution: 2.4→34.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5466 0 160 99 5725
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015874HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.178010HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1980SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes165HARMONIC2
X-RAY DIFFRACTIONt_gen_planes856HARMONIC5
X-RAY DIFFRACTIONt_it5874HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion21.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion730SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6508SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.48 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3159 145 4.89 %
Rwork0.2742 2821 -
all0.2764 2966 -
obs--98.23 %
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)
14.37741.0889-2.84251.3554-0.446.2391-0.06250.1039-0.4670.1218-0.37310.0005-0.1416-0.89570.4356-0.2421-0.0101-0.0285-0.1077-0.0843-0.2251-13.0799-9.5961-16.8635
21.3337-1.7391-0.94366.2382-0.07953.02820.01140.17010.10450.4618-0.04530.2153-0.5468-0.41270.03390.23280.34490.1419-0.13360.0181-0.3564-24.337322.7034-11.849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|360 }
2X-RAY DIFFRACTION2{ B|1 - B|350 }

+
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://pdbjlvh1.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