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- PDB-7f7g: a linear Peptide Inhibitors in complex with GK domain -

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Basic information

Entry
Database: PDB / ID: 7f7g
Titlea linear Peptide Inhibitors in complex with GK domain
Components
  • DLG4 GK domain
  • UNK-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYS-ALA-ILE-GLN-UNK
KeywordsPEPTIDE BINDING PROTEIN / MAGUK DLG stapled peptide linear peptide
Function / homology
Function and homology information


RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / structural constituent of postsynaptic density / synaptic vesicle maturation / positive regulation of neuron projection arborization ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / structural constituent of postsynaptic density / synaptic vesicle maturation / positive regulation of neuron projection arborization / regulation of grooming behavior / receptor localization to synapse / vocalization behavior / cerebellar mossy fiber / LGI-ADAM interactions / proximal dendrite / neuron spine / Trafficking of AMPA receptors / protein localization to synapse / AMPA glutamate receptor clustering / cellular response to potassium ion / Activation of Ca-permeable Kainate Receptor / dendritic branch / positive regulation of dendrite morphogenesis / dendritic spine morphogenesis / negative regulation of receptor internalization / juxtaparanode region of axon / frizzled binding / acetylcholine receptor binding / neuron projection terminus / dendritic spine organization / regulation of NMDA receptor activity / positive regulation of synapse assembly / Synaptic adhesion-like molecules / NMDA selective glutamate receptor signaling pathway / RAF/MAP kinase cascade / beta-2 adrenergic receptor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / social behavior / locomotory exploration behavior / AMPA glutamate receptor complex / regulation of neuronal synaptic plasticity / neuromuscular process controlling balance / kinesin binding / excitatory synapse / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / D1 dopamine receptor binding / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / dendrite cytoplasm / cell periphery / PDZ domain binding / establishment of protein localization / regulation of long-term neuronal synaptic plasticity / synaptic membrane / postsynaptic density membrane / neuromuscular junction / cerebral cortex development / cell-cell adhesion / kinase binding / cell junction / synaptic vesicle / cell-cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / protein-containing complex assembly / scaffold protein binding / protein phosphatase binding / chemical synaptic transmission / dendritic spine / postsynaptic membrane / postsynapse / neuron projection / postsynaptic density / signaling receptor binding / synapse / dendrite / protein-containing complex binding / protein kinase binding / glutamatergic synapse / endoplasmic reticulum / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. ...Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Disks large homolog 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.446 Å
AuthorsShang, Y. / Huang, X. / Li, X. / Zhang, M.
Funding support Hong Kong, 5items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)17309616 Hong Kong
The University Grants Committee, Research Grants Council (RGC)T13-605/18-W Hong Kong
The University Grants Committee, Research Grants Council (RGC)AoE/M-09/12 Hong Kong
The University Grants Committee, Research Grants Council (RGC)AoE/P-705/16 Hong Kong
The University Grants Committee, Research Grants Council (RGC)ITCPD/17-9 Hong Kong
CitationJournal: Rsc Chem Biol / Year: 2021
Title: Entropy of stapled peptide inhibitors in free state is the major contributor to the improvement of binding affinity with the GK domain.
Authors: Unarta, I.C. / Xu, J. / Shang, Y. / Cheung, C.H.P. / Zhu, R. / Chen, X. / Cao, S. / Cheung, P.P. / Bierer, D. / Zhang, M. / Huang, X. / Li, X.
History
DepositionJun 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DLG4 GK domain
B: DLG4 GK domain
C: UNK-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYS-ALA-ILE-GLN-UNK
D: UNK-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYS-ALA-ILE-GLN-UNK


Theoretical massNumber of molelcules
Total (without water)46,5894
Polymers46,5894
Non-polymers00
Water3,567198
1
A: DLG4 GK domain
C: UNK-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYS-ALA-ILE-GLN-UNK


Theoretical massNumber of molelcules
Total (without water)23,2942
Polymers23,2942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-0 kcal/mol
Surface area11090 Å2
MethodPISA
2
B: DLG4 GK domain
D: UNK-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYS-ALA-ILE-GLN-UNK


Theoretical massNumber of molelcules
Total (without water)23,2942
Polymers23,2942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-2 kcal/mol
Surface area10780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.854, 61.579, 103.851
Angle α, β, γ (deg.)90.000, 98.290, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain D
21chain C
12(chain A and ((resid 530 and (name O or name...
22(chain B and (resseq 530:531 or (resid 532 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ACEACENH2NH2chain DDD-6 - 71 - 14
211ACEACENH2NH2chain CCC-6 - 71 - 14
112PHEPHEPHEPHE(chain A and ((resid 530 and (name O or name...AA5306
122SERSERGLYGLY(chain A and ((resid 530 and (name O or name...AA528 - 7134 - 189
132SERSERGLYGLY(chain A and ((resid 530 and (name O or name...AA528 - 7134 - 189
142SERSERGLYGLY(chain A and ((resid 530 and (name O or name...AA528 - 7134 - 189
152SERSERGLYGLY(chain A and ((resid 530 and (name O or name...AA528 - 7134 - 189
212PHEPHEVALVAL(chain B and (resseq 530:531 or (resid 532 and (name...BB530 - 5316 - 7
222HISHISHISHIS(chain B and (resseq 530:531 or (resid 532 and (name...BB5328
232PHEPHESERSER(chain B and (resseq 530:531 or (resid 532 and (name...BB530 - 7126 - 188
242PHEPHESERSER(chain B and (resseq 530:531 or (resid 532 and (name...BB530 - 7126 - 188
252PHEPHESERSER(chain B and (resseq 530:531 or (resid 532 and (name...BB530 - 7126 - 188

NCS ensembles :
ID
1
2

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Components

#1: Protein DLG4 GK domain


Mass: 21690.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg4, Dlgh4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P31016
#2: Protein/peptide UNK-ARG-ILE-ARG-ARG-ASP-GLU-TYR-LEU-LYS-ALA-ILE-GLN-UNK


Mass: 1603.869 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: (0.02 M Citric acid, 0.08 M BIS-TRIS propane / pH 8.8), 16% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97774 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.09
ReflectionResolution: 2.4446→50 Å / Num. obs: 15628 / % possible obs: 93.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 8.5
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 777 / % possible all: 96.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UAT

3uat


Resolution: 2.446→35.479 Å / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 32.2 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2561 850 5.44 %
Rwork0.201 14796 -
obs0.2039 15618 93.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.67 Å2 / Biso mean: 37.9771 Å2 / Biso min: 11.14 Å2
Refinement stepCycle: final / Resolution: 2.446→35.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 0 198 3408
Biso mean---36.09 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083270
X-RAY DIFFRACTIONf_angle_d1.0714403
X-RAY DIFFRACTIONf_chiral_restr0.058476
X-RAY DIFFRACTIONf_plane_restr0.007583
X-RAY DIFFRACTIONf_dihedral_angle_d23.1391998
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11D118X-RAY DIFFRACTION7.054TORSIONAL
12C118X-RAY DIFFRACTION7.054TORSIONAL
21A1623X-RAY DIFFRACTION7.054TORSIONAL
22B1623X-RAY DIFFRACTION7.054TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.447-2.59990.3311260.26352453257989
2.5999-2.80.33821280.2542489261790
2.8-3.08060.31311290.23152496262591
3.0806-3.52370.28621470.19872484263190
3.5237-4.42930.21731180.16422468258688
4.4293-18.44710.21731440.18372406255085
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)
17.3554.4584-3.74174.7614-1.83215.65780.55180.01730.87860.41410.19790.8675-0.4406-0.6899-0.28050.31030.11210.04850.2770.04460.2222-7.9711-0.30014.0719
20.3243-0.27250.37161.10320.39561.016-0.0023-0.104-0.2681-0.16770.18680.128-0.4055-0.12480.0540.2087-0.0524-0.02630.17580.06520.3542-2.61910.56050.9777
31.70970.0920.852.6820.39281.3231-0.0477-0.2705-0.01990.4989-0.042-0.44160.02140.2697-0.00270.23770.0244-0.05050.28010.00850.314210.69910.645815.8304
42.164-0.09011.58661.64861.09591.69610.0669-0.4114-0.11370.0548-0.0602-0.16280.111-0.2004-0.01060.2079-0.00470.00180.24550.06320.35180.81872.46459.7805
53.67180.2399-1.23472.00780.03531.2621-0.25040.2589-0.21850.179-0.02560.04150.7526-0.5029-0.10560.2759-0.0476-0.0360.1242-0.00760.207-0.0702-4.0379-3.131
64.45942.3347-1.24955.868-3.43376.4196-0.01840.2317-0.2125-0.4008-0.0722-0.38850.03160.20530.15210.21120.0526-0.00180.2142-0.0540.24510.8316-0.3965-12.3081
74.1564-1.22870.73936.8045-0.09532.1770.308-0.0427-0.3161-0.1341-0.19660.6806-0.1207-0.1563-0.03810.2021-0.0187-0.03470.1487-0.00580.2641-6.17630.343-9.8038
82.7550.4606-1.934.8645-0.83671.4183-0.3161-0.3304-0.0763-0.21460.5318-0.4844-0.31820.5523-0.25630.27130.0055-0.03570.2695-0.12040.271815.68164.541753.707
92.0621-1.14381.7851.7989-0.1462.7304-0.24520.42810.04180.0850.28070.32440.5946-0.02910.02750.2616-0.04430.00720.19210.07530.310212.3657-5.582546.6534
101.2002-0.643-0.33382.00190.96221.4538-0.2299-0.23220.01320.17080.1695-0.02230.20480.15220.03760.23540.00230.00350.22360.04320.2527.5184-10.878462.0539
110.7896-0.3684-0.48423.71430.38921.1854-0.0166-0.09340.35371.2524-0.01110.2178-0.0026-0.39320.05960.42550.0385-0.01730.2815-0.04170.2362-1.5217-2.426771.3729
120.09260.2397-0.21481.33990.41571.31870.109-0.06160.13230.5111-0.02570.47870.0417-0.10370.06950.26360.07170.02870.2870.00660.3714-1.7381.085163.8238
135.44420.472-2.91510.7403-0.04594.150.4346-0.6982-0.33280.1355-0.09230.55430.06110.9368-0.12710.31250.0081-0.06110.16490.03770.33359.3563-1.065165.0786
143.7009-0.9172-1.06252.6037-0.11572.61880.3421-0.57150.52360.03320.27050.2959-0.2785-0.2372-0.22410.27360.02870.0740.2846-0.03450.36019.86265.692957.5933
152.66220.2863-0.55392.0667-0.34770.1581-0.4272-0.11620.8886-0.0846-0.0572-0.108-0.9405-0.2401-0.22770.3448-0.0060.01650.2239-0.04410.276610.54818.943748.2835
163.11691.47580.31916.49843.54475.3057-0.12810.67640.0347-0.24310.35150.7966-0.0766-0.2340.04490.2423-0.0646-0.05520.35740.05330.3583-0.12185.413139.2132
173.0274-0.82830.14414.93330.60521.62310.27090.1648-0.2739-0.0677-0.1994-0.13170.03980.2672-0.14710.2689-0.0371-0.03590.2792-0.02730.214616.47584.48541.3749
186.2027-0.6024-3.60165.126-1.97823.292-0.210.55080.0456-0.6691-0.2035-0.25580.01980.1903-0.03020.2817-0.1415-0.13730.26460.05310.32726.416215.26424.2804
193.1486-0.12770.61274.3544-0.47564.8769-0.88120.435-0.3847-0.4415-0.85980.14030.2429-0.014-0.63520.3056-0.03460.10370.2624-0.00330.40434.0653-10.393655.7324
205.46084.67442.474.54643.42414.27660.40780.6684-0.2843-1.0323-0.4782-0.1666-1.0993-0.50530.03930.4940.1133-0.11090.3151-0.04350.4745-1.5416-3.086755.0164
213.2382.4303-2.33312.3284-2.7633.7511-0.53771.0556-0.0021-1.29060.2548-0.56220.48510.17930.06140.368-0.08730.0860.32360.02360.331812.09378.22163.7238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 528 through 543 )A528 - 543
2X-RAY DIFFRACTION2chain 'A' and (resid 544 through 566 )A544 - 566
3X-RAY DIFFRACTION3chain 'A' and (resid 567 through 606 )A567 - 606
4X-RAY DIFFRACTION4chain 'A' and (resid 607 through 640 )A607 - 640
5X-RAY DIFFRACTION5chain 'A' and (resid 641 through 654 )A641 - 654
6X-RAY DIFFRACTION6chain 'A' and (resid 655 through 687 )A655 - 687
7X-RAY DIFFRACTION7chain 'A' and (resid 688 through 713 )A688 - 713
8X-RAY DIFFRACTION8chain 'B' and (resid 530 through 543 )B530 - 543
9X-RAY DIFFRACTION9chain 'B' and (resid 544 through 554 )B544 - 554
10X-RAY DIFFRACTION10chain 'B' and (resid 555 through 579 )B555 - 579
11X-RAY DIFFRACTION11chain 'B' and (resid 580 through 594 )B580 - 594
12X-RAY DIFFRACTION12chain 'B' and (resid 595 through 606 )B595 - 606
13X-RAY DIFFRACTION13chain 'B' and (resid 607 through 622 )B607 - 622
14X-RAY DIFFRACTION14chain 'B' and (resid 623 through 640 )B623 - 640
15X-RAY DIFFRACTION15chain 'B' and (resid 641 through 654 )B641 - 654
16X-RAY DIFFRACTION16chain 'B' and (resid 655 through 687 )B655 - 687
17X-RAY DIFFRACTION17chain 'B' and (resid 688 through 712 )B688 - 712
18X-RAY DIFFRACTION18chain 'C' and (resid -5 through 0 )C-5 - 0
19X-RAY DIFFRACTION19chain 'D' and (resid -5 through 0 )D-5 - 0
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 6 )D1 - 6
21X-RAY DIFFRACTION21chain 'C' and (resid 1 through 6)C1 - 6

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