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- PDB-3zxt: Dimeric structure of DAPK-1 catalytic domain in complex with AMPP... -

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Basic information

Entry
Database: PDB / ID: 3zxt
TitleDimeric structure of DAPK-1 catalytic domain in complex with AMPPCP- Mg
ComponentsDEATH-ASSOCIATED PROTEIN KINASE 1
KeywordsTRANSFERASE / APOPTOSIS / ATP BINDING
Function / homology
Function and homology information


cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Caspase activation via Dependence Receptors in the absence of ligand / defense response to tumor cell / regulation of NMDA receptor activity / calcium/calmodulin-dependent protein kinase activity / syntaxin-1 binding / extrinsic apoptotic signaling pathway via death domain receptors ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Caspase activation via Dependence Receptors in the absence of ligand / defense response to tumor cell / regulation of NMDA receptor activity / calcium/calmodulin-dependent protein kinase activity / syntaxin-1 binding / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / apoptotic signaling pathway / cellular response to type II interferon / actin cytoskeleton / protein autophosphorylation / regulation of apoptotic process / calmodulin binding / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of translation / postsynaptic density / intracellular signal transduction / regulation of autophagy / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / GTP binding / glutamatergic synapse / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat ...Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Death-associated protein kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
Authorsde Diego, I. / Lehmann, F. / Wilmanns, M.
CitationJournal: To be Published
Title: A Journey Through the Dap Kinase Architecture
Authors: De Diego, I. / Kuper, J. / Lehmann, F. / Wilmanns, M.
History
DepositionAug 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEATH-ASSOCIATED PROTEIN KINASE 1
B: DEATH-ASSOCIATED PROTEIN KINASE 1
C: DEATH-ASSOCIATED PROTEIN KINASE 1
D: DEATH-ASSOCIATED PROTEIN KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,06814
Polymers130,9014
Non-polymers2,16710
Water2,306128
1
A: DEATH-ASSOCIATED PROTEIN KINASE 1
B: DEATH-ASSOCIATED PROTEIN KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5588
Polymers65,4512
Non-polymers1,1086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-68.3 kcal/mol
Surface area24600 Å2
MethodPISA
2
C: DEATH-ASSOCIATED PROTEIN KINASE 1
D: DEATH-ASSOCIATED PROTEIN KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5106
Polymers65,4512
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-48.8 kcal/mol
Surface area24690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.407, 76.578, 106.892
Angle α, β, γ (deg.)90.00, 92.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.854084, -0.140235, -0.500873), (0.06402, -0.983989, 0.166333), (-0.51618, 0.109996, 0.849388)192.76007, -4.55571, 53.71389
3given(-0.826397, 0.038017, 0.561803), (-0.076379, -0.996065, -0.044947), (0.557884, -0.080054, 0.826049)91.92567, 19.83395, -27.4805

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Components

#1: Protein
DEATH-ASSOCIATED PROTEIN KINASE 1 / DAP KINASE 1


Mass: 32725.262 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.95 Å3/Da / Density % sol: 58.39 % / Description: NONE
Crystal growDetails: 0.1 M HEPES PH7.0, 0.1M MGCL2, 15% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9235
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 5, 2011 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9235 Å / Relative weight: 1
ReflectionResolution: 2.65→45.71 Å / Num. obs: 39321 / % possible obs: 99.8 % / Observed criterion σ(I): 2.5 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.5 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W4J

2w4j


Resolution: 2.65→106.83 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.893 / SU B: 29.35 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R: 0.694 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2846 1976 5 %RANDOM
Rwork0.21601 ---
obs0.21947 37331 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.865 Å2
Baniso -1Baniso -2Baniso -3
1--3.04 Å20 Å20.33 Å2
2--5.96 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.65→106.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7674 0 130 128 7932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.027951
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.98910828
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2555989
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77525.223337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.897151254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.081523
X-RAY DIFFRACTIONr_chiral_restr0.1050.21253
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215907
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 131 -
Rwork0.351 2649 -
obs--99.86 %
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)
12.2391-0.18650.44511.7822-0.17412.07180.1015-0.01990.1389-0.1009-0.1150.3211-0.1927-0.09620.01350.2421-0.02340.01060.4888-0.08380.343632.47019.03558.3143
22.92280.1395-0.89380.03850.1736.26150.03940.3950.0117-0.07420.031-0.0546-0.339-0.0741-0.07040.2774-0.01770.0260.0636-0.04850.280869.21417.538450.5384
30.8880.3720.23620.25190.68187.41360.10740.1861-0.178-0.03840.0472-0.04970.2698-0.4977-0.15460.2361-0.0306-0.03670.58390.06860.318671.07426.4302-2.6122
43.4190.5409-0.05011.0559-0.30951.36930.0797-0.3640.17410.082-0.11490.04560.02910.21260.03530.2404-0.073-0.00420.1836-0.01730.3217107.31274.381760.2766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C5 - 276
2X-RAY DIFFRACTION2A7 - 276
3X-RAY DIFFRACTION3D7 - 276
4X-RAY DIFFRACTION4B7 - 276

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