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- PDB-1ndl: THE AWD NUCLEOTIDE DIPHOSPHATE KINASE FROM DROSOPHILA -

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Basic information

Entry
Database: PDB / ID: 1ndl
TitleTHE AWD NUCLEOTIDE DIPHOSPHATE KINASE FROM DROSOPHILA
ComponentsNUCLEOSIDE DIPHOSPHATE KINASE
KeywordsPHOSPHOTRANSFERASE
Function / homology
Function and homology information


ribonucleoside triphosphate biosynthetic process / regulation of tube architecture, open tracheal system / Azathioprine ADME / Ribavirin ADME / establishment or maintenance of polarity of follicular epithelium / open tracheal system development / epithelial cell migration, open tracheal system / Interconversion of nucleotide di- and triphosphates / deoxyribonucleoside triphosphate biosynthetic process / nuclear microtubule ...ribonucleoside triphosphate biosynthetic process / regulation of tube architecture, open tracheal system / Azathioprine ADME / Ribavirin ADME / establishment or maintenance of polarity of follicular epithelium / open tracheal system development / epithelial cell migration, open tracheal system / Interconversion of nucleotide di- and triphosphates / deoxyribonucleoside triphosphate biosynthetic process / nuclear microtubule / Neutrophil degranulation / nucleoside-diphosphate kinase / nucleotide metabolic process / adherens junction organization / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / microtubule-based process / kinase activity / mitotic cell cycle / microtubule binding / microtubule / GTP binding / magnesium ion binding / mitochondrion / ATP binding / plasma membrane
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
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsJanin, J. / Chiadmi, M. / Dumas, C. / Lascu, I. / Lebras, G. / Morera, S. / Veron, M.
Citation
Journal: Structure / Year: 1993
Title: Crystal structure of the Awd nucleotide diphosphate kinase from Drosophila.
Authors: Chiadmi, M. / Morera, S. / Lascu, I. / Dumas, C. / Le Bras, G. / Veron, M. / Janin, J.
#1: Journal: Biochemistry / Year: 1994
Title: Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase
Authors: Morera, S. / Lascu, I. / Dumas, C. / Lebras, G. / Briozzo, P. / Veron, M. / Janin, J.
#2: Journal: Embo J. / Year: 1992
Title: X-Ray Structure of Nucleoside Diphosphate Kinase
Authors: Dumas, C. / Lascu, I. / Morera, S. / Glaser, P. / Fourme, R. / Wallet, V. / Lacombe, M.L. / Veron, M. / Janin, J.
History
DepositionNov 27, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE
C: NUCLEOSIDE DIPHOSPHATE KINASE


Theoretical massNumber of molelcules
Total (without water)51,5733
Polymers51,5733
Non-polymers00
Water5,675315
1
A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE
C: NUCLEOSIDE DIPHOSPHATE KINASE

A: NUCLEOSIDE DIPHOSPHATE KINASE
B: NUCLEOSIDE DIPHOSPHATE KINASE
C: NUCLEOSIDE DIPHOSPHATE KINASE


Theoretical massNumber of molelcules
Total (without water)103,1456
Polymers103,1456
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_766-x+2,-x+y+1,-z+5/31
Buried area16850 Å2
ΔGint-80 kcal/mol
Surface area35580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)115.650, 115.650, 98.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: ELECTRON DENSITY IS ABSENT FOR MET 1 AND POOR FOR ALA 2 IN ALL THREE CHAINS.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.35556, 0.91736, 0.17896), (0.0661, -0.2157, 0.97423), (0.93231, -0.3346, -0.1373)12.95289, -42.1394, 17.32422
2given(0.34473, 0.06154, 0.93668), (0.92061, -0.2171, -0.3245), (0.18339, 0.97421, -0.1315)-17.225, -16.298, 40.09089
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX 3* RECORDS BELOW WILL GENERATE THE HEXAMER FROM THE TRIMER PRESENTED IN THE ENTRY.

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Components

#1: Protein NUCLEOSIDE DIPHOSPHATE KINASE


Mass: 17190.852 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / References: UniProt: P08879, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.65 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.4→10 Å / σ(F): 1 /
RfactorNum. reflection
obs0.167 27564
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3609 0 0 315 3924
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3171
X-RAY DIFFRACTIONp_mcangle_it2.171.5
X-RAY DIFFRACTIONp_scbond_it1.851
X-RAY DIFFRACTIONp_scangle_it3.131.5
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.1430.15
X-RAY DIFFRACTIONp_singtor_nbd0.1770.3
X-RAY DIFFRACTIONp_multtor_nbd0.260.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1740.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.5993
X-RAY DIFFRACTIONp_staggered_tor17.4915
X-RAY DIFFRACTIONp_orthonormal_tor20.2820
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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