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- PDB-6ke5: Structure of CavAb in complex with Diltiazem and Amlodipine -

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Basic information

Entry
Database: PDB / ID: 6ke5
TitleStructure of CavAb in complex with Diltiazem and Amlodipine
ComponentsIon transport protein
KeywordsMEMBRANE PROTEIN / Voltage gated Ion Channel / Voltage-gated Calcium Channel / Block / Tetrameric
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity / metal ion binding / identical protein binding
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
amlodipine / Chem-D6C / SN-GLYCEROL-3-PHOSPHATE / [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri RM4018 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsTang, L.
CitationJournal: Mol.Pharmacol. / Year: 2019
Title: Structural Basis for Diltiazem Block of a Voltage-Gated Ca2+Channel.
Authors: Tang, L. / Gamal El-Din, T.M. / Lenaeus, M.J. / Zheng, N. / Catterall, W.A.
History
DepositionJul 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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: Ion transport protein
B: Ion transport protein
C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,04117
Polymers131,8314
Non-polymers3,21013
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16520 Å2
ΔGint-144 kcal/mol
Surface area48660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.730, 124.990, 191.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Ion transport protein


Mass: 32957.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri RM4018 (bacteria) / Strain: RM4018 / Gene: Abu_1752 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5

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Non-polymers , 6 types, 14 molecules

#2: Chemical ChemComp-LPC / [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE


Mass: 468.585 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H47NO7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H9O6P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-6UB / amlodipine / ~{O}3-ethyl ~{O}5-methyl (4~{S})-2-(2-azanylethoxymethyl)-4-(2-chlorophenyl)-6-methyl-1,4-dihydropyridine-3,5-dicarboxylate


Mass: 408.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25ClN2O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-D6C / [(2~{S},3~{R})-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxidanylidene-2,3-dihydro-1,5-benzothiazepin-3-yl] ethanoate


Mass: 414.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26N2O4S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 5.67 Å3/Da / Density % sol: 78.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M Na-citrate,pH5.0,2M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→44.706 Å / Num. obs: 66929 / % possible obs: 90.8 % / Redundancy: 4.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 9478 / CC1/2: 0.861 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.803→44.706 Å / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.48 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2921 3532 5.28 %
Rwork0.2486 63571 -
obs0.2522 66882 90.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 244.37 Å2 / Biso mean: 80.8363 Å2 / Biso min: 20.69 Å2
Refinement stepCycle: final / Resolution: 2.803→44.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7402 0 173 1 7576
Biso mean--59.28 48.72 -
Num. residues----902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0167769
X-RAY DIFFRACTIONf_angle_d1.70510558
X-RAY DIFFRACTIONf_chiral_restr0.1451262
X-RAY DIFFRACTIONf_plane_restr0.0121243
X-RAY DIFFRACTIONf_dihedral_angle_d21.3122695
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8032-2.85150.30441410.3433016315782
2.8515-2.90330.34411780.3423081325984
2.9033-2.95920.31261550.32723157331287
2.9592-3.01950.36311370.32083214335188
3.0195-3.08510.3131920.28773165335786
3.0851-3.15690.34131700.29243201337187
3.1569-3.23580.33881560.28863192334887
3.2358-3.32320.29781800.25493219339987
3.3232-3.42090.2871610.24323219338087
3.4209-3.53130.27311640.2363214337887
3.5313-3.65740.28951890.23013173336286
3.6574-3.80360.25541560.23823248340488
3.8036-3.97650.26231740.23493182335687
3.9765-4.18590.29631640.24623246341087
4.1859-4.44770.28641550.25283212336787
4.4477-4.79050.25571740.23123199337386
4.7905-5.27120.30831530.22313200335386
5.2712-6.0310.32811740.24643189336384
6.031-7.5870.3131670.27493113328082
7.587-36.3380.26091440.22433131327579

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