[English] 日本語
Yorodumi
- PDB-3cuk: Crystal structure of human D-amino acid oxidase: bound to an inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cuk
TitleCrystal structure of human D-amino acid oxidase: bound to an inhibitor
ComponentsD-amino-acid oxidaseD-amino acid oxidase
KeywordsOXIDOREDUCTASE / ALPHA-BETA-ALPHA MOTIF / FLAVIN CONTAINING PROTEINALPHA-BETA-ALPHA MOTIF / FLAVIN CONTAINING PROTEIN / FAD / Flavoprotein / Peroxisome
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-amino acid catabolic process / D-serine 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-amino acid catabolic process / D-serine 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 / cytosol / cytoplasm
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
4H-furo[3,2-b]pyrrole-5-carboxylic acid / FLAVIN-ADENINE DINUCLEOTIDE / D-amino-acid oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsPrasad, S. / Munshi, S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: The discovery of fused pyrrole carboxylic acids as novel, potent D-amino acid oxidase (DAO) inhibitors.
Authors: Sparey, T. / Abeywickrema, P. / Almond, S. / Brandon, N. / Byrne, N. / Campbell, A. / Hutson, P.H. / Jacobson, M. / Jones, B. / Munshi, S. / Pascarella, D. / Pike, A. / Prasad, G.S. / Sachs, ...Authors: Sparey, T. / Abeywickrema, P. / Almond, S. / Brandon, N. / Byrne, N. / Campbell, A. / Hutson, P.H. / Jacobson, M. / Jones, B. / Munshi, S. / Pascarella, D. / Pike, A. / Prasad, G.S. / Sachs, N. / Sakatis, M. / Sardana, V. / Venkatraman, S. / Young, M.B.
History
DepositionApr 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 14, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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
C: D-amino-acid oxidase
D: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,83012
Polymers158,0844
Non-polymers3,7478
Water75742
1
A: D-amino-acid oxidase
C: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9156
Polymers79,0422
Non-polymers1,8734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-amino-acid oxidase
D: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9156
Polymers79,0422
Non-polymers1,8734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: D-amino-acid oxidase
hetero molecules

C: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9156
Polymers79,0422
Non-polymers1,8734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6160 Å2
ΔGint-27.4 kcal/mol
Surface area26050 Å2
MethodPISA
4
B: D-amino-acid oxidase
hetero molecules

D: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9156
Polymers79,0422
Non-polymers1,8734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6120 Å2
ΔGint-29.9 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.729, 51.145, 153.294
Angle α, β, γ (deg.)90.00, 110.45, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
D-amino-acid oxidase / D-amino acid oxidase / DAMOX / DAO / DAAO


Mass: 39520.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAO, DAMOX / Plasmid: pRSET / 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 / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-4P5 / 4H-furo[3,2-b]pyrrole-5-carboxylic acid


Mass: 151.119 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H5NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 15% PEG 3350, 0.15M POTASSIUM TRICITR TRIS-HCL, pH 7.80, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: Feb 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 46710 / % possible obs: 96.8 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 11
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.1.24refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VE9

1ve9


Resolution: 2.49→42.52 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.888 / SU B: 29.033 / SU ML: 0.317 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 2.129 / ESU R Free: 0.417 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3285 2362 5.1 %RANDOM
Rwork0.23893 ---
obs0.24342 44300 96.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.324 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å21.04 Å2
2---0.75 Å20 Å2
3---3.04 Å2
Refinement stepCycle: LAST / Resolution: 2.49→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10552 0 256 42 10850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.02211124
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6651.9715164
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5351296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53723.383532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.765151756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6781580
X-RAY DIFFRACTIONr_chiral_restr0.1560.21608
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028524
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2750.25084
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3310.27210
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2428
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0651.56746
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.757210460
X-RAY DIFFRACTIONr_scbond_it2.82735497
X-RAY DIFFRACTIONr_scangle_it4.2354.54704
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.492→2.557 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 177 -
Rwork0.314 3176 -
obs--93.19 %
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)
12.2670.77310.63441.78820.43271.1195-0.091-0.0585-0.10280.04360.07280.1152-0.00690.00680.0182-0.08890.05720.0422-0.09520.009-0.0885-24.0734-24.986911.4283
22.4399-0.84640.55651.644-0.42441.0258-0.07050.1489-0.0875-0.07520.0482-0.1120.0051-0.0030.0223-0.0985-0.05320.0406-0.0933-0.046-0.0312-2.7239-51.135960.3799
32.376-1.0332-0.01952.3927-0.05031.0002-0.02370.1916-0.0684-0.016-0.03630.1399-0.12360.00560.06-0.0418-0.0545-0.027-0.0204-0.0078-0.1406-16.5074-17.2953-20.9848
42.59230.94580.19172.38220.21061.0555-0.0747-0.2621-0.04860.02120.0528-0.1867-0.136-0.01070.0219-0.03690.0564-0.0359-0.055-0.0108-0.0884-10.2694-43.484792.783
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3371 - 337
2X-RAY DIFFRACTION2BB1 - 3371 - 337
3X-RAY DIFFRACTION3CC1 - 3371 - 337
4X-RAY DIFFRACTION4DD1 - 3371 - 337

+
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