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- PDB-3dls: Crystal structure of human PAS kinase bound to ADP -

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Basic information

Entry
Database: PDB / ID: 3dls
TitleCrystal structure of human PAS kinase bound to ADP
ComponentsPAS domain-containing serine/threonine-protein kinase
KeywordsTRANSFERASE / PAS KINASE / PASK / PROTEIN KINASE / DRUG DISCOVERY / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


regulation of glucagon secretion / negative regulation of glycogen biosynthetic process / regulation of respiratory gaseous exchange / energy homeostasis / phosphatidylinositol binding / positive regulation of translation / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation ...regulation of glucagon secretion / negative regulation of glycogen biosynthetic process / regulation of respiratory gaseous exchange / energy homeostasis / phosphatidylinositol binding / positive regulation of translation / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
PAS domain / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...PAS domain / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PAS domain-containing serine/threonine-protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsAntonysamy, S. / Bonanno, J.B. / Romero, R. / Russell, M. / Iizuka, M. / Gheyi, T. / Wasserman, S.R. / Rutter, J. / Sauder, J.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural bases of PAS domain-regulated kinase (PASK) activation in the absence of activation loop phosphorylation.
Authors: Kikani, C.K. / Antonysamy, S.A. / Bonanno, J.B. / Romero, R. / Zhang, F.F. / Russell, M. / Gheyi, T. / Iizuka, M. / Emtage, S. / Sauder, J.M. / Turk, B.E. / Burley, S.K. / Rutter, J.
History
DepositionJun 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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.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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PAS domain-containing serine/threonine-protein kinase
B: PAS domain-containing serine/threonine-protein kinase
C: PAS domain-containing serine/threonine-protein kinase
D: PAS domain-containing serine/threonine-protein kinase
E: PAS domain-containing serine/threonine-protein kinase
F: PAS domain-containing serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,27731
Polymers227,2526
Non-polymers3,02525
Water5,044280
1
A: PAS domain-containing serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4006
Polymers37,8751
Non-polymers5245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PAS domain-containing serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4006
Polymers37,8751
Non-polymers5245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PAS domain-containing serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4006
Polymers37,8751
Non-polymers5245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: PAS domain-containing serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3755
Polymers37,8751
Non-polymers5004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: PAS domain-containing serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3514
Polymers37,8751
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: PAS domain-containing serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3514
Polymers37,8751
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
A: PAS domain-containing serine/threonine-protein kinase
B: PAS domain-containing serine/threonine-protein kinase
C: PAS domain-containing serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,19918
Polymers113,6263
Non-polymers1,57315
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-162 kcal/mol
Surface area38530 Å2
MethodPISA
8
D: PAS domain-containing serine/threonine-protein kinase
hetero molecules

E: PAS domain-containing serine/threonine-protein kinase
hetero molecules

F: PAS domain-containing serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,07813
Polymers113,6263
Non-polymers1,45210
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_465x-1,y+1,z1
Buried area6620 Å2
ΔGint-123 kcal/mol
Surface area37970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.778, 85.840, 94.154
Angle α, β, γ (deg.)77.280, 77.500, 60.090
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PAS domain-containing serine/threonine-protein kinase / PAS-kinase / PASKIN / hPASK


Mass: 37875.270 Da / Num. of mol.: 6 / Fragment: PROTEIN KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PASK, KIAA0135 / Production host: BACULOVIRUS / Strain (production host): SF9
References: UniProt: Q96RG2, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 10% GLYCEROL, 18% PEG 3350, 150 mM CALCIUM ACETATE, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 22, 2008
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 96809

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementHighest resolution: 2.3 Å / Occupancy max: 1 / Occupancy min: 1
RfactorNum. reflection
Rfree0.297 -
Rwork0.241 -
all0.244 96809
obs0.244 96809
Displacement parametersBiso max: 81.99 Å2 / Biso mean: 37.365 Å2 / Biso min: 2.72 Å2
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13263 0 181 280 13724

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