[English] 日本語
Yorodumi
- PDB-4wsq: Crystal Structure of Adaptor Protein 2 Associated Kinase (AAK1) i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wsq
TitleCrystal Structure of Adaptor Protein 2 Associated Kinase (AAK1) in complex with small molecule inhibitor
ComponentsAP2-associated protein kinase 1
KeywordsTRANSFERASE / kinase / small-molecule / catalytic domain / protein kinase / protein binding / protein kinase inhibitors
Function / homology
Function and homology information


regulation of clathrin-dependent endocytosis / presynaptic endocytosis / AP-2 adaptor complex binding / membrane organization / Notch binding / clathrin-coated vesicle / positive regulation of Notch signaling pathway / cell leading edge / clathrin-coated pit / terminal bouton ...regulation of clathrin-dependent endocytosis / presynaptic endocytosis / AP-2 adaptor complex binding / membrane organization / Notch binding / clathrin-coated vesicle / positive regulation of Notch signaling pathway / cell leading edge / clathrin-coated pit / terminal bouton / Cargo recognition for clathrin-mediated endocytosis / regulation of protein localization / presynapse / Clathrin-mediated endocytosis / protein stabilization / non-specific serine/threonine protein kinase / protein phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
: / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily ...: / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
K-252A / AP2-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSorrell, F.J. / Elkins, J.M. / Krojer, T. / Williams, E. / Abdul, K. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Sorrell, F.J. / Elkins, J.M. / Krojer, T. / Williams, E. / Abdul, K. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2016
Title: Family-wide Structural Analysis of Human Numb-Associated Protein Kinases.
Authors: Sorrell, F.J. / Szklarz, M. / Abdul Azeez, K.R. / Elkins, J.M. / Knapp, S.
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Mar 9, 2016Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jan 10, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AP2-associated protein kinase 1
B: AP2-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,87811
Polymers71,4882
Non-polymers1,3899
Water5,134285
1
A: AP2-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4706
Polymers35,7441
Non-polymers7265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AP2-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4085
Polymers35,7441
Non-polymers6644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.660, 71.320, 183.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LYSLYSchain AAA29 - 3451 - 317
2ALAALAchain BBB33 - 3425 - 314
Detailsunit 1

-
Components

#1: Protein AP2-associated protein kinase 1 / Adaptor-associated kinase 1


Mass: 35744.090 Da / Num. of mol.: 2 / Fragment: kinase domain, UNP residues 29-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AAK1, KIAA1048 / Plasmid: pNIC-CTH0 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): R3
References: UniProt: Q2M2I8, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-KSA / K-252A


Mass: 467.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H21N3O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.005M zinc acetate, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.95→56.33 Å / Num. obs: 66564 / % possible obs: 99.9 % / Redundancy: 4.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.05 / Net I/σ(I): 8.3 / Num. measured all: 310951 / Scaling rejects: 32
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.95-24.81.0942.12093343790.7940.535100
9.15-56.334.20.0382030757380.9970.02198.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.2.17data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2buj

2buj


Resolution: 1.95→56.325 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 3225 4.85 %Random selection
Rwork0.1809 63212 --
obs0.1821 66437 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.15 Å2 / Biso mean: 43.5603 Å2 / Biso min: 20.97 Å2
Refinement stepCycle: final / Resolution: 1.95→56.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4841 0 80 285 5206
Biso mean--28.52 45.56 -
Num. residues----627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135101
X-RAY DIFFRACTIONf_angle_d1.2736967
X-RAY DIFFRACTIONf_chiral_restr0.063785
X-RAY DIFFRACTIONf_plane_restr0.007896
X-RAY DIFFRACTIONf_dihedral_angle_d12.841829
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2775X-RAY DIFFRACTION5.886TORSIONAL
12B2775X-RAY DIFFRACTION5.886TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.97910.35231250.303927312856100
1.9791-2.010.33281590.29626612820100
2.01-2.0430.28381350.281727302865100
2.043-2.07820.27421560.253926972853100
2.0782-2.1160.30641320.240327082840100
2.116-2.15670.29061350.231727302865100
2.1567-2.20080.2631350.226127222857100
2.2008-2.24860.25921480.204126882836100
2.2486-2.30090.23731450.187927292874100
2.3009-2.35850.24361580.190626942852100
2.3585-2.42220.22321490.186427032852100
2.4222-2.49350.21191390.181827162855100
2.4935-2.5740.22911350.17527402875100
2.574-2.6660.22561450.17727682913100
2.666-2.77270.23341340.180827272861100
2.7727-2.89890.22551650.18427222887100
2.8989-3.05170.19691430.181527482891100
3.0517-3.24290.1871020.18628242926100
3.2429-3.49330.19811180.187427802898100
3.4933-3.84470.19511450.160827842929100
3.8447-4.40090.16161620.151527752937100
4.4009-5.54390.15891250.14528542979100
5.5439-56.34860.17561350.16482981311699
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)
10.87040.4837-0.0842.2357-0.67641.7816-0.0530.0319-0.0481-0.07310.0063-0.02490.01850.04380.03840.34440.0304-0.0030.1873-0.01960.24843.0307-14.7644-41.5051
21.1956-0.25140.75182.0424-0.32771.7085-0.12120.16140.1573-0.2306-0.0452-0.10990.03080.0650.14740.4099-0.01460.01510.30380.03750.272-3.4734-11.9255-92.291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 29:345)A29 - 345
2X-RAY DIFFRACTION2(chain B and resseq 33:342)B33 - 342

+
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