[English] 日本語
Yorodumi
- PDB-4l4m: Structural Analysis of a Phosphoribosylated Inhibitor in Complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l4m
TitleStructural Analysis of a Phosphoribosylated Inhibitor in Complex with Human Nicotinamide Phosphoribosyltransferase
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTransferase/Transferase Inhibitor / Transferase / Inhibitor / active site / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


nicotinamide phosphoribosyltransferase activity / nicotinamide phosphoribosyltransferase / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / : / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression ...nicotinamide phosphoribosyltransferase activity / nicotinamide phosphoribosyltransferase / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / : / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression / cell junction / cell-cell signaling / nuclear speck / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / cytosol
Similarity search - Function
Nicotinamide phosphoribosyl transferase / Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinate/nicotinamide phosphoribosyltransferase / Nicotinate phosphoribosyltransferase (NAPRTase) family / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-1XD / PHOSPHATE ION / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.445 Å
AuthorsOh, A. / Ho, Y. / Zak, M. / Liu, Y. / Yuen, P. / Zheng, X. / Dragovich, S.P. / Wang, W.
CitationJournal: Chembiochem / Year: 2014
Title: Structural and biochemical analyses of the catalysis and potency impact of inhibitor phosphoribosylation by human nicotinamide phosphoribosyltransferase.
Authors: Oh, A. / Ho, Y.C. / Zak, M. / Liu, Y. / Chen, X. / Yuen, P.W. / Zheng, X. / Liu, Y. / Dragovich, P.S. / Wang, W.
History
DepositionJun 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Nicotinamide phosphoribosyltransferase
B: Nicotinamide phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,24410
Polymers113,8852
Non-polymers1,3598
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9980 Å2
ΔGint-61 kcal/mol
Surface area32820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.579, 107.056, 82.998
Angle α, β, γ (deg.)90.00, 96.47, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Nicotinamide phosphoribosyltransferase / NAmPRTase / Nampt / Pre-B-cell colony-enhancing factor 1 / Pre-B cell-enhancing factor / Visfatin


Mass: 56942.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAMPT, PBEF, PBEF1 / Production host: Escherichia coli (E. coli)
References: UniProt: P43490, nicotinamide phosphoribosyltransferase
#2: Chemical ChemComp-1XD / N-{4-[(3,5-difluorophenyl)sulfonyl]benzyl}imidazo[1,2-a]pyridine-7-carboxamide


Mass: 427.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H15F2N3O3S
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 0.2uL + 0.2uL drops containing 6mg/mL Nampt, 0.1M Sodium phosphate, 25-29% polyethylene glycol 3350, 0.2M NaCl, 1mM ligand compound, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K, ...Details: 0.2uL + 0.2uL drops containing 6mg/mL Nampt, 0.1M Sodium phosphate, 25-29% polyethylene glycol 3350, 0.2M NaCl, 1mM ligand compound, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2013
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.445→50 Å / Num. all: 38931 / Num. obs: 37802 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.45→2.54 Å / % possible all: 96.2

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.445→37.098 Å / SU ML: 0.39 / σ(F): 0.66 / Phase error: 26.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 3614 4.98 %5% random
Rwork0.2079 ---
all0.2101 39746 --
obs0.2101 37652 94.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10.159 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-18.0574 Å20 Å27.2632 Å2
2--11.2776 Å20 Å2
3---8.7852 Å2
Refinement stepCycle: LAST / Resolution: 2.445→37.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7524 0 88 269 7881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037788
X-RAY DIFFRACTIONf_angle_d0.70110555
X-RAY DIFFRACTIONf_dihedral_angle_d11.7042855
X-RAY DIFFRACTIONf_chiral_restr0.051146
X-RAY DIFFRACTIONf_plane_restr0.0031337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4453-2.47750.41321280.32532568X-RAY DIFFRACTION94
2.4775-2.51140.38311500.31292691X-RAY DIFFRACTION93
2.5114-2.54730.311530.29742562X-RAY DIFFRACTION93
2.5473-2.58530.37441240.29842583X-RAY DIFFRACTION93
2.5853-2.62570.33091240.31632633X-RAY DIFFRACTION92
2.6257-2.66870.36311620.29412617X-RAY DIFFRACTION94
2.6687-2.71470.34861140.29392555X-RAY DIFFRACTION93
2.7147-2.76410.32941150.3112580X-RAY DIFFRACTION90
2.7641-2.81720.37161240.30412437X-RAY DIFFRACTION89
2.8172-2.87470.43861540.27982663X-RAY DIFFRACTION94
2.8747-2.93720.26311350.25032703X-RAY DIFFRACTION96
2.9372-3.00550.28081060.21892770X-RAY DIFFRACTION97
3.0055-3.08060.22181540.21232713X-RAY DIFFRACTION97
3.0806-3.16390.24451430.2062663X-RAY DIFFRACTION96
3.1639-3.25690.27731750.22082639X-RAY DIFFRACTION97
3.2569-3.3620.23111460.21582757X-RAY DIFFRACTION96
3.362-3.48210.22121360.17612638X-RAY DIFFRACTION96
3.4821-3.62140.16661350.18462713X-RAY DIFFRACTION96
3.6214-3.7860.19531620.17192641X-RAY DIFFRACTION95
3.786-3.98540.22691460.16382620X-RAY DIFFRACTION93
3.9854-4.23480.23851180.16912544X-RAY DIFFRACTION92
4.2348-4.56120.21361330.14542759X-RAY DIFFRACTION98
4.5612-5.01920.19341380.14752756X-RAY DIFFRACTION98
5.0192-5.74320.22021360.17332731X-RAY DIFFRACTION98
5.7432-7.22710.24031700.20382660X-RAY DIFFRACTION96
7.2271-37.1020.20191330.17962715X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 13.5098 Å / Origin y: 1.0711 Å / Origin z: 22.4897 Å
111213212223313233
T-0.0362 Å2-0.0147 Å2-0.0121 Å2--0.0314 Å20.024 Å2---0.0532 Å2
L0.1113 °20.0248 °20.0202 °2-0.1169 °20.0177 °2--0.0657 °2
S0.0243 Å °-0.0502 Å °0.0322 Å °-0.0461 Å °0.001 Å °-0.1158 Å °-0.0111 Å °0.1041 Å °0.045 Å °
Refinement TLS groupSelection details: chain A or chain B or chain S or chain L

+
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