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- PDB-1z83: Crystal structure of human AK1A in complex with AP5A -

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Basic information

Entry
Database: PDB / ID: 1z83
TitleCrystal structure of human AK1A in complex with AP5A
ComponentsAdenylate kinase 1
KeywordsTRANSFERASE / adenylate kinase / humna / AP5A / diadenosine pentaphosphate / nucleotide kinase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


nucleoside-phosphate kinase / dAMP kinase activity / outer dense fiber / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / AMP kinase activity / nucleobase-containing small molecule interconversion / nucleoside-diphosphate kinase ...nucleoside-phosphate kinase / dAMP kinase activity / outer dense fiber / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / adenylate kinase / AMP kinase activity / nucleobase-containing small molecule interconversion / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / nucleoside diphosphate kinase activity / ATP metabolic process / extracellular exosome / ATP binding / cytoplasm / cytosol
Similarity search - Function
Adenylate kinase isoenzyme 1 / Adenylate kinase, isozyme 1/5 / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenylate kinase isoenzyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFilippakopoulos, P. / Bunkoczi, G. / Jansson, A. / Schreurs, A. / Knapp, S. / Edwards, A. / von Delft, F. / Sundstrom, M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human AK1A in complex with AP5A
Authors: Filippakopoulos, P. / Bunkoczi, G. / Jansson, A. / Schreurs, A. / Knapp, S. / Edwards, A. / von Delft, F. / Sundstrom, M.
History
DepositionMar 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylate kinase 1
B: Adenylate kinase 1
C: Adenylate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,07417
Polymers65,5143
Non-polymers3,56114
Water8,251458
1
A: Adenylate kinase 1
B: Adenylate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,12412
Polymers43,6762
Non-polymers2,44810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-208 kcal/mol
Surface area17130 Å2
MethodPISA
2
B: Adenylate kinase 1
C: Adenylate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,09312
Polymers43,6762
Non-polymers2,41710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Adenylate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9515
Polymers21,8381
Non-polymers1,1134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.194, 46.259, 119.576
Angle α, β, γ (deg.)90.00, 116.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-645-

ZN

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 1 - 194 / Label seq-ID: 2 - 195

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
DetailsThree monomers in the asymmetric unit

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Components

#1: Protein Adenylate kinase 1 / ATP-AMP transphosphorylase / AK1 / Myokinase


Mass: 21837.957 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AK1 / Plasmid: hak1a-pLIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P00568, adenylate kinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MES, PEG550, Zinksulphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 49395 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 21.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 9.9 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
EVAL15data reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.698 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21832 2379 5.1 %RANDOM
Rwork0.16916 ---
obs0.17166 44688 95.31 %-
all-44688 --
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: 19.457 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å2-0.41 Å2
2--2.4 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4471 0 194 458 5123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224755
X-RAY DIFFRACTIONr_bond_other_d0.0010.024340
X-RAY DIFFRACTIONr_angle_refined_deg1.6222.0366453
X-RAY DIFFRACTIONr_angle_other_deg0.851310092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1645592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86924.011187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67915855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3561535
X-RAY DIFFRACTIONr_chiral_restr0.080.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025117
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02898
X-RAY DIFFRACTIONr_nbd_refined0.2110.2950
X-RAY DIFFRACTIONr_nbd_other0.180.24362
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22272
X-RAY DIFFRACTIONr_nbtor_other0.0820.22651
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2346
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.210
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1620.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it232990
X-RAY DIFFRACTIONr_mcbond_other0.65731220
X-RAY DIFFRACTIONr_mcangle_it2.71954678
X-RAY DIFFRACTIONr_scbond_it4.90982010
X-RAY DIFFRACTIONr_scangle_it6.538111770
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1129medium positional0.220.5
2B1129medium positional0.190.5
3C1129medium positional0.20.5
1A1673loose positional0.555
2B1673loose positional0.475
3C1673loose positional0.595
1A1129medium thermal0.932
2B1129medium thermal0.822
3C1129medium thermal0.92
1A1673loose thermal2.0710
2B1673loose thermal1.710
3C1673loose thermal2.0410
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 178 -
Rwork0.214 2989 -
obs--87.22 %
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)
11.7744-0.3707-0.16590.90490.06721.0860.0150.02620.0523-0.00190.0010.0038-0.0196-0.0484-0.0159-0.0844-0.0072-0.0038-0.1999-0.0203-0.082517.979545.83710.5029
21.9710.48230.30531.35080.24591.50760.032-0.3023-0.0040.0181-0.0289-0.007-0.0095-0.0354-0.0031-0.0735-0.0029-0.0016-0.0319-0.0152-0.0826.730447.268235.1792
32.554-0.4605-0.01331.48690.16881.9836-0.04920.04810.0547-0.0602-0.0211-0.0111-0.0047-0.02030.0704-0.0553-0.0092-0.0005-0.0833-0.0201-0.079442.741247.297435.8303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1941 - 195
2X-RAY DIFFRACTION2BB0 - 1941 - 195
3X-RAY DIFFRACTION3CC0 - 1941 - 195

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