[English] 日本語
Yorodumi
- PDB-2ch6: Crystal structure of human N-acetylglucosamine kinase in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ch6
TitleCrystal structure of human N-acetylglucosamine kinase in complex with ADP and glucose
ComponentsN-ACETYL-D-GLUCOSAMINE KINASE
KeywordsTRANSFERASE / SUGAR KINASE / RIBONUCLEASE H FOLD / SUGAR KINASE/HSP70/ACTIN SUPERFAMILY
Function / homology
Function and homology information


muramyl dipeptide kinase activity / N-acetylglucosamine kinase / N-acetylglucosamine kinase activity / N-acetylmannosamine metabolic process / N-acylmannosamine kinase / N-acetylglucosamine catabolic process / Synthesis of UDP-N-acetyl-glucosamine / N-acetylglucosamine metabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway ...muramyl dipeptide kinase activity / N-acetylglucosamine kinase / N-acetylglucosamine kinase activity / N-acetylmannosamine metabolic process / N-acylmannosamine kinase / N-acetylglucosamine catabolic process / Synthesis of UDP-N-acetyl-glucosamine / N-acetylglucosamine metabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / N-acetylneuraminate catabolic process / UDP-N-acetylglucosamine biosynthetic process / response to muramyl dipeptide / defense response to bacterium / innate immune response / extracellular exosome / ATP binding / cytosol
Similarity search - Function
N-acetyl-D-glucosamine kinase NAGK-like / ATPase, BadF/BadG/BcrA/BcrD type / BadF/BadG/BcrA/BcrD ATPase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / alpha-D-glucopyranose / N-acetyl-D-glucosamine kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.72 Å
AuthorsWeihofen, W.A. / Berger, M. / Chen, H. / Saenger, W. / Hinderlich, S.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structures of Human N-Acetylglucosamine Kinase in Two Complexes with N-Acetylglucosamine and with Adp/Glucose: Insights Into Substrate Specificity and Regulation.
Authors: Weihofen, W.A. / Berger, M. / Chen, H. / Saenger, W. / Hinderlich, S.
History
DepositionMar 13, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / software / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _software.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-ACETYL-D-GLUCOSAMINE KINASE
B: N-ACETYL-D-GLUCOSAMINE KINASE
C: N-ACETYL-D-GLUCOSAMINE KINASE
D: N-ACETYL-D-GLUCOSAMINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,10012
Polymers149,6704
Non-polymers2,4298
Water00
1
A: N-ACETYL-D-GLUCOSAMINE KINASE
D: N-ACETYL-D-GLUCOSAMINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0506
Polymers74,8352
Non-polymers1,2154
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-24.7 kcal/mol
Surface area29710 Å2
MethodPISA
2
B: N-ACETYL-D-GLUCOSAMINE KINASE
C: N-ACETYL-D-GLUCOSAMINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0506
Polymers74,8352
Non-polymers1,2154
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-25.7 kcal/mol
Surface area29530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.710, 101.992, 110.181
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.96727, -0.18627, -0.17233), (0.2353, -0.91261, -0.33432), (-0.095, -0.36393, 0.92657)154.22133, 128.66124, -33.4981
2given(-0.78777, 0.46701, -0.40165), (-0.60797, -0.48475, 0.6288), (0.09895, 0.73954, 0.6658)68.0626, 60.03337, -48.91132
3given(-0.9293, -0.34685, 0.12688), (-0.34543, 0.69471, -0.63092), (0.13068, -0.63014, -0.7654)144.12819, 89.39929, 162.9726
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO NAGK DIMERS (CHAINS AD FORM ONE, AND CHAINS C AND B FORM THE OTHER).

-
Components

#1: Protein
N-ACETYL-D-GLUCOSAMINE KINASE / N-ACETYLGLUCOSAMINE KINASE / NAGK PROTEIN / PROTEIN TMP_LOCUS_2 / GLCNAC KINASE


Mass: 37417.609 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: CDNA FROM THE RESOURCE CENTER OF THE GERMAN HUMAN GENOME PROJECT
Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UJ70, N-acetylglucosamine kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 51.9 %
Description: MAD DATA OF SEMET LABELED CRYSTALS WERE COLLECTED AT PROTEIN STRUCTURE FACTORY BEAMLINE BL2 OF FREE UNIVERSITY BERLIN AT BESSY
Crystal growpH: 5.6
Details: 100 MM MES PH5.6, 100 MM NACL, 2% (W/V) PEG 20K, pH 5.60

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.72→30 Å / Num. obs: 40858 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.2
Reflection shellResolution: 2.72→2.96 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.8 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: MAD / Resolution: 2.72→29.8 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.878 / SU B: 27.79 / SU ML: 0.32 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2093 5.1 %RANDOM
Rwork0.227 ---
obs0.231 39284 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.67 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å20 Å20 Å2
2--2.77 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.72→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10159 0 156 0 10315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210536
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9814255
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54451322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16623.178450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.843151699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0891574
X-RAY DIFFRACTIONr_chiral_restr0.0970.21556
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027946
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.24525
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.27096
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.2163
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4991.56712
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.884210380
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.14634363
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.854.53875
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.72→2.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 161 -
Rwork0.3 2824 -
obs--100 %
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)
11.8193-0.9054-0.59494.8985-0.26882.28040.1787-0.1090.2859-0.0371-0.0518-0.2583-0.2158-0.0243-0.1268-0.2909-0.02390.0367-0.32110.0251-0.110135.04794.34574.0381
21.71360.8461-0.27723.5827-1.90073.17290.1919-0.707-0.6430.7613-0.3027-0.21830.2628-0.25270.11080.2913-0.1224-0.08540.3930.1797-0.019315.682560.8839115.2026
34.1743-2.3728-0.41835.24550.26362.38780.03390.8609-0.6549-0.5973-0.2481-0.09290.74640.4760.21420.1106-0.00480.03160.31210.0016-0.041797.846414.7428132.0132
41.9865-0.6426-0.15446.8708-2.75972.67790.0934-0.06390.1411-0.32830.10530.536-0.14950.0751-0.1987-0.1366-0.0157-0.0839-0.1667-0.09770.014689.113797.5949.4314
52.83010.2377-1.42331.57450.73882.9101-0.1245-0.1446-0.12180.12370.0103-0.00170.31850.12630.1142-0.18360.0613-0.0776-0.28230.0134-0.215553.089375.357867.1176
65.84331.64211.95512.18590.84653.51040.2322-0.5362-0.9272-0.0297-0.0727-0.43030.08470.0629-0.1595-0.14340.06520.0108-0.14130.1504-0.04114.138771.06993.3072
73.2665-0.1271.45561.36330.00943.3798-0.10840.67920.1848-0.1378-0.1258-0.0942-0.21120.19040.2342-0.0953-0.08180.0044-0.02650.0988-0.182575.71330.7812128.5244
85.2709-0.4112-1.89421.5860.36133.3683-0.0441-0.85890.20410.08250.0814-0.1041-0.11350.4415-0.0373-0.16720.0419-0.0934-0.1245-0.0603-0.212776.188781.979371.8776
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 119
2X-RAY DIFFRACTION1A334 - 344
3X-RAY DIFFRACTION2B3 - 119
4X-RAY DIFFRACTION2B334 - 344
5X-RAY DIFFRACTION3C3 - 119
6X-RAY DIFFRACTION3C334 - 344
7X-RAY DIFFRACTION4D3 - 119
8X-RAY DIFFRACTION4D334 - 344
9X-RAY DIFFRACTION5A120 - 291
10X-RAY DIFFRACTION6B120 - 291
11X-RAY DIFFRACTION7C120 - 291
12X-RAY DIFFRACTION8D120 - 291

+
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