[English] 日本語
Yorodumi
- PDB-5dhs: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dhs
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a novel inhibitor
ComponentsNAD kinase 1
KeywordsTRANSFERASE / tetrameric NAD kinase
Function / homology
Function and homology information


NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / NAD metabolic process / NAD binding / phosphorylation / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / Probable inorganic polyphosphate/atp-NAD kinase; domain 2 / ATP-NAD kinase C-terminal domain / NAD kinase / ATP-NAD kinase, PpnK-type, C-terminal / ATP-NAD kinase N-terminal domain / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / Tumour Suppressor Smad4 / Sandwich ...Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / Probable inorganic polyphosphate/atp-NAD kinase; domain 2 / ATP-NAD kinase C-terminal domain / NAD kinase / ATP-NAD kinase, PpnK-type, C-terminal / ATP-NAD kinase N-terminal domain / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / Tumour Suppressor Smad4 / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-5AG / CITRIC ACID / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsGelin, M. / Paoletti, J. / Assairi, L. / Huteau, V. / Pochet, S. / Labesse, G.
CitationJournal: Eur.J.Med.Chem. / Year: 2016
Title: 8-Thioalkyl-adenosine derivatives inhibit Listeria monocytogenes NAD kinase through a novel binding mode.
Authors: Paoletti, J. / Assairi, L. / Gelin, M. / Huteau, V. / Nahori, M.A. / Dussurget, O. / Labesse, G. / Pochet, S.
History
DepositionAug 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD kinase 1
B: NAD kinase 1
C: NAD kinase 1
D: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,69611
Polymers124,1814
Non-polymers2,5157
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint-45 kcal/mol
Surface area40890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.770, 118.950, 66.900
Angle α, β, γ (deg.)90.000, 100.140, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1METMETASPASPchain AAA1 - 2641 - 264
2METMETHISHISchain BBB1 - 2671 - 267
3METMETGLUGLUchain CCC1 - 2631 - 263
4LYSLYSGLUGLUchain DDD2 - 2632 - 263

-
Components

#1: Protein
NAD kinase 1 / ATP-dependent NAD kinase / Inorganic polyphosphate/ATP-NAD kinase 1


Mass: 31045.279 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Gene: nadK1, lmo0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-5AG / 5'-azido-5'-deoxy-8-[(2-{[2-(3-ethynylphenyl)ethyl]amino}-2-oxoethyl)sulfanyl]adenosine


Mass: 509.541 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H23N9O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 30 mM sodium bromide, 220 mM potassium citrate, pH 4.8-5.1, glycerol 6%, 15-16% w/v polyethylene glycol 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.62→65.855 Å / Num. all: 30967 / Num. obs: 30967 / % possible obs: 100 % / Redundancy: 2.6 % / Biso Wilson estimate: 49.1 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.063 / Rsym value: 0.045 / Net I/av σ(I): 12.759 / Net I/σ(I): 12.5 / Num. measured all: 80726
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.62-2.762.70.3512.21203444920.3020.3511.9100
2.76-2.932.70.25431138042810.2240.2542.6100
2.93-3.132.60.1525.11050939880.1350.1524.2100
3.13-3.382.60.0888.6971737510.0780.0887.2100
3.38-3.712.60.04716.2885134440.040.04712.8100
3.71-4.142.60.0323.8807731100.0260.0318.5100
4.14-4.782.60.0224.2724827620.0170.0226.1100
4.78-5.862.60.0232.5592423160.0170.0226.9100
5.86-8.292.50.02127.5454818140.0180.02128.599.9
8.29-44.1392.40.01917243810090.0170.01936.699.2

-
Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2i1w

2i1w


Resolution: 2.62→44.139 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 32.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2776 1910 3.14 %
Rwork0.2425 58876 -
obs0.2437 30967 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 210.2 Å2 / Biso mean: 73.6062 Å2 / Biso min: 13.11 Å2
Refinement stepCycle: final / Resolution: 2.62→44.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8071 0 176 173 8420
Biso mean--59.54 46.43 -
Num. residues----1030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058449
X-RAY DIFFRACTIONf_angle_d0.75611437
X-RAY DIFFRACTIONf_chiral_restr0.0291247
X-RAY DIFFRACTIONf_plane_restr0.0021456
X-RAY DIFFRACTIONf_dihedral_angle_d11.7483024
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4709X-RAY DIFFRACTION11.296TORSIONAL
12B4709X-RAY DIFFRACTION11.296TORSIONAL
13C4709X-RAY DIFFRACTION11.296TORSIONAL
14D4709X-RAY DIFFRACTION11.296TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.62-2.68550.42591370.44193433099
2.6855-2.75810.42671170.38134195431299
2.7581-2.83930.40121290.372642394368100
2.8393-2.93090.36391250.351141894314100
2.9309-3.03560.40911450.325342184363100
3.0356-3.15710.29421490.297841784327100
3.1571-3.30080.3051300.271342154345100
3.3008-3.47470.28051670.245541744341100
3.4747-3.69240.24391450.216142364381100
3.6924-3.97730.23131200.21742294349100
3.9773-4.37720.26261550.188741614316100
4.3772-5.00980.2081340.176342164350100
5.0098-6.30890.24651340.214642054339100
6.3089-44.14510.26791230.2342284351100
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)
13.47821.0397-1.28695.2761-2.11443.34970.2078-0.4172-0.56330.7735-0.4101-0.1010.27810.15030.16580.7253-0.1243-0.00980.32950.03460.42315.289-30.4644-25.9485
22.94531.8091-0.93213.4345-0.79653.22280.2073-0.07850.02870.4775-0.14720.232-0.0788-0.2345-0.07770.3077-0.01560.01080.216-0.05430.26619.8662-6.4075-38.457
33.53051.31160.78731.47810.70171.66230.9553-1.38431.23540.5888-0.174-0.0905-0.70890.301-0.11210.9758-0.8084-0.01821.1046-0.30880.862535.367117.9311-23.777
43.06460.1444-0.180.96530.1833.34230.1911-0.4697-0.42390.4214-0.1606-0.78320.00350.9081-0.07580.4086-0.1182-0.21450.61080.14660.737534.4519-6.7894-33.6573
53.9247-0.4922.21432.8913-1.54133.65190.32540.77110.9139-0.9479-0.03410.5216-1.0093-0.6443-0.13690.91790.35090.07050.95060.32220.78816.12348.505-77.2942
64.13070.886-0.56973.66580.08233.13110.11680.7879-0.2977-0.2398-0.0782-0.03460.101-0.2288-0.00880.380.1885-0.01590.5-0.09230.303415.5584-12.9741-64.4097
78.3301-3.1039-3.613.63462.88114.77720.130.7657-0.6874-0.1164-0.55060.11560.75860.42520.2240.66240.37390.01621.2479-0.0830.810351.4171-23.9281-68.3525
82.13980.0788-0.09622.89230.52192.30370.2160.52870.1171-0.1398-0.1243-0.9128-0.10930.6774-0.20040.29980.10930.0850.66030.11490.59338.1317-3.2113-60.7062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:100)A1 - 100
2X-RAY DIFFRACTION2(chain A and resid 101:264)A101 - 264
3X-RAY DIFFRACTION3(chain B and resid 1:100)B1 - 100
4X-RAY DIFFRACTION4(chain B and resid 101:264)B101 - 264
5X-RAY DIFFRACTION5(chain C and resid 1:100)C1 - 100
6X-RAY DIFFRACTION6(chain C and resid 101:264)C101 - 264
7X-RAY DIFFRACTION7(chain D and resid 1:100)D1 - 100
8X-RAY DIFFRACTION8(chain D and resid 101:264)D101 - 264

+
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