[English] 日本語
Yorodumi
- PDB-5ui4: Structure of NME1 covalently conjugated to imidazole fluorosulfate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ui4
TitleStructure of NME1 covalently conjugated to imidazole fluorosulfate
ComponentsNucleoside diphosphate kinase A
KeywordsTRANSFERASE / arylfluorosulfate / covalent / kinase
Function / homology
Function and homology information


DNA nuclease activity / Ribavirin ADME / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / Azathioprine ADME / nucleoside diphosphate kinase activity / positive regulation of DNA binding / GTP biosynthetic process ...DNA nuclease activity / Ribavirin ADME / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / Azathioprine ADME / nucleoside diphosphate kinase activity / positive regulation of DNA binding / GTP biosynthetic process / ribosomal small subunit binding / lactation / 3'-5' exonuclease activity / positive regulation of epithelial cell proliferation / ruffle membrane / endocytosis / nervous system development / regulation of apoptotic process / cell differentiation / early endosome / negative regulation of cell population proliferation / GTP binding / magnesium ion binding / RNA binding / extracellular exosome / ATP binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A7Z / Nucleoside diphosphate kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMortenson, D.E. / Brighty, G.J. / Wilson, I.A. / Kelly, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
George E. Hewitt Foundation for Medical Research United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: "Inverse Drug Discovery" Strategy To Identify Proteins That Are Targeted by Latent Electrophiles As Exemplified by Aryl Fluorosulfates.
Authors: Mortenson, D.E. / Brighty, G.J. / Plate, L. / Bare, G. / Chen, W. / Li, S. / Wang, H. / Cravatt, B.F. / Forli, S. / Powers, E.T. / Sharpless, K.B. / Wilson, I.A. / Kelly, J.W.
History
DepositionJan 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoside diphosphate kinase A
B: Nucleoside diphosphate kinase A
C: Nucleoside diphosphate kinase A
D: Nucleoside diphosphate kinase A
E: Nucleoside diphosphate kinase A
F: Nucleoside diphosphate kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,10312
Polymers108,7856
Non-polymers2,3186
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15660 Å2
ΔGint-101 kcal/mol
Surface area33650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.462, 68.058, 69.682
Angle α, β, γ (deg.)113.65, 98.20, 112.46
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEAA13 - 15020 - 157
21ILEILEBB13 - 15020 - 157
12TYRTYRAA13 - 15120 - 158
22TYRTYRCC13 - 15120 - 158
13ILEILEAA13 - 15020 - 157
23ILEILEDD13 - 15020 - 157
14TYRTYRAA13 - 15120 - 158
24TYRTYREE13 - 15120 - 158
15TYRTYRAA13 - 15120 - 158
25TYRTYRFF13 - 15120 - 158
16ILEILEBB13 - 15020 - 157
26ILEILECC13 - 15020 - 157
17GLUGLUBB13 - 15220 - 159
27GLUGLUDD13 - 15220 - 159
18ILEILEBB13 - 15020 - 157
28ILEILEEE13 - 15020 - 157
19ILEILEBB13 - 15020 - 157
29ILEILEFF13 - 15020 - 157
110ILEILECC13 - 15020 - 157
210ILEILEDD13 - 15020 - 157
111TYRTYRCC13 - 15120 - 158
211TYRTYREE13 - 15120 - 158
112TYRTYRCC13 - 15120 - 158
212TYRTYRFF13 - 15120 - 158
113ILEILEDD13 - 15020 - 157
213ILEILEEE13 - 15020 - 157
114ILEILEDD13 - 15020 - 157
214ILEILEFF13 - 15020 - 157
115TYRTYREE13 - 15120 - 158
215TYRTYRFF13 - 15120 - 158

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

#1: Protein
Nucleoside diphosphate kinase A / NDP kinase A / Granzyme A-activated DNase / GAAD / Metastasis inhibition factor nm23 / NM23-H1 / ...NDP kinase A / Granzyme A-activated DNase / GAAD / Metastasis inhibition factor nm23 / NM23-H1 / Tumor metastatic process-associated protein


Mass: 18130.799 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NME1, NDPKA, NM23 / Production host: Escherichia coli (E. coli) / References: UniProt: P15531, nucleoside-diphosphate kinase
#2: Chemical
ChemComp-A7Z / 4-[4-(3-methoxyphenyl)-1-(prop-2-yn-1-yl)-1H-imidazol-5-yl]phenyl sulfurofluoridate


Mass: 386.397 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H15FN2O4S
#3: Water ChemComp-HOH / water


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 4.7 mg/mL solution protein-fluorosulfate conjugate combined with solution containing 0.2 M NaCl, 0.1 M HEPES pH 7.5 and 30% (v/v) PEG400 in sitting drops. Crystals frozen in LN2 stream ...Details: 4.7 mg/mL solution protein-fluorosulfate conjugate combined with solution containing 0.2 M NaCl, 0.1 M HEPES pH 7.5 and 30% (v/v) PEG400 in sitting drops. Crystals frozen in LN2 stream without additional cryoprotectant

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→59.81 Å / Num. obs: 22132 / % possible obs: 96.7 % / Redundancy: 2.6 % / Biso Wilson estimate: 34.1 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.101 / Rsym value: 0.128 / Net I/σ(I): 7.7
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.4 / CC1/2: 0.63 / Rpim(I) all: 0.606 / Rsym value: 0.763 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HVE

2hve


Resolution: 2.75→59.81 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 19.323 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22314 1134 5.1 %RANDOM
Rwork0.19338 ---
obs0.19493 20995 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.126 Å2
Baniso -1Baniso -2Baniso -3
1--3.02 Å21.15 Å20.17 Å2
2---0.18 Å21.63 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 2.75→59.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7118 0 156 99 7373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197461
X-RAY DIFFRACTIONr_bond_other_d0.0040.027067
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.93510077
X-RAY DIFFRACTIONr_angle_other_deg1.183316238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7925880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73223.913345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.804151260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6831548
X-RAY DIFFRACTIONr_chiral_restr0.070.21053
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028993
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021767
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9855.9323580
X-RAY DIFFRACTIONr_mcbond_other1.9855.9323579
X-RAY DIFFRACTIONr_mcangle_it3.2848.8954465
X-RAY DIFFRACTIONr_mcangle_other3.2848.8954466
X-RAY DIFFRACTIONr_scbond_it2.1266.1993881
X-RAY DIFFRACTIONr_scbond_other2.1256.1993882
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6449.2195612
X-RAY DIFFRACTIONr_long_range_B_refined5.50146.6588016
X-RAY DIFFRACTIONr_long_range_B_other5.49646.678003
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A161080.05
12B161080.05
21A161500.05
22C161500.05
31A159880.06
32D159880.06
41A162920.05
42E162920.05
51A161420.06
52F161420.06
61B160120.05
62C160120.05
71B161720.06
72D161720.06
81B160900.05
82E160900.05
91B160300.06
92F160300.06
101C158580.05
102D158580.05
111C161180.05
112E161180.05
121C162440.05
122F162440.05
131D159860.05
132E159860.05
141D158920.05
142F158920.05
151E161240.06
152F161240.06
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 91 -
Rwork0.341 1511 -
obs--96.56 %

+
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