[English] 日本語
Yorodumi
- PDB-1yc2: Sir2Af2-NAD-ADPribose-nicotinamide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yc2
TitleSir2Af2-NAD-ADPribose-nicotinamide
ComponentsNAD-dependent deacetylase 2
KeywordsHYDROLASE / sir2 / sirtuin / nicotinamide / NAD / ADPribose / ternary complex
Function / homology
Function and homology information


protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / protein acetyllysine N-acetyltransferase / histone deacetylase activity, NAD-dependent / NAD+ binding / zinc ion binding / cytoplasm
Similarity search - Function
Sirtuin, class U / Sirtuin, class III / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. ...Sirtuin, class U / Sirtuin, class III / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NICOTINAMIDE / TRIETHYLENE GLYCOL / NAD-dependent protein deacylase 2
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAvalos, J.L. / Bever, M.K. / Wolberger, C.
CitationJournal: Mol.Cell / Year: 2005
Title: Mechanism of Sirtuin Inhibition by Nicotinamide: Altering the NAD(+) Cosubstrate Specificity of a Sir2 Enzyme.
Authors: Avalos, J.L. / Bever, K.M. / Wolberger, C.
History
DepositionDec 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: NAD-dependent deacetylase 2
B: NAD-dependent deacetylase 2
C: NAD-dependent deacetylase 2
D: NAD-dependent deacetylase 2
E: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,54243
Polymers142,6855
Non-polymers6,85738
Water4,486249
1
A: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,83210
Polymers28,5371
Non-polymers1,2959
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,37612
Polymers28,5371
Non-polymers1,83911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0348
Polymers28,5371
Non-polymers1,4977
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8948
Polymers28,5371
Non-polymers1,3577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4065
Polymers28,5371
Non-polymers8694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: NAD-dependent deacetylase 2
hetero molecules

A: NAD-dependent deacetylase 2
B: NAD-dependent deacetylase 2
C: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,13638
Polymers114,1484
Non-polymers5,98834
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_554x,y,z-11
identity operation1_555x,y,z1
Buried area19820 Å2
ΔGint-286 kcal/mol
Surface area40370 Å2
MethodPISA
7
A: NAD-dependent deacetylase 2
C: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,86618
Polymers57,0742
Non-polymers2,79216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-145 kcal/mol
Surface area22070 Å2
MethodPISA
8
B: NAD-dependent deacetylase 2
hetero molecules

D: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,27020
Polymers57,0742
Non-polymers3,19618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area8100 Å2
ΔGint-120 kcal/mol
Surface area22470 Å2
MethodPISA
9
A: NAD-dependent deacetylase 2
B: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,20822
Polymers57,0742
Non-polymers3,13420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-116 kcal/mol
Surface area22450 Å2
MethodPISA
10
C: NAD-dependent deacetylase 2
hetero molecules

D: NAD-dependent deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,92816
Polymers57,0742
Non-polymers2,85414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area7330 Å2
ΔGint-93 kcal/mol
Surface area22350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.122, 181.562, 79.025
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
NAD-dependent deacetylase 2 / Regulatory protein SIR2 homolog 2 / SIR2-Af2


Mass: 28537.006 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: npdA2 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS
References: UniProt: O30124, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

-
Non-polymers , 10 types, 287 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical
ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H6N2O
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: HEPES, ammonium sulfate, PEG400, nicotinamide, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.099997 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2003
RadiationMonochromator: 2 CRYSTAL SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.099997 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 59851 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.108 / Rsym value: 0.086 / Net I/σ(I): 19.7
Reflection shellResolution: 2.4→2.49 Å / % possible all: 82.1

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 3011 -RANDOM
Rwork0.2093 ---
all0.2122 59933 --
obs0.2118 59360 97.3 %-
Displacement parametersBiso mean: 44.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9745 0 415 249 10409
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006476
X-RAY DIFFRACTIONc_angle_deg1.23416

+
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