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- PDB-6dn6: SPRY domain-containing SOCS box protein 2 complexed with INNN(ABU... -

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Basic information

Entry
Database: PDB / ID: 6dn6
TitleSPRY domain-containing SOCS box protein 2 complexed with INNN(ABU) cyclic peptide inhibitor
Components
  • INNN(ABU) cyclic peptide inhibitor
  • SPRY domain-containing SOCS box protein 2
KeywordsIMMUNE SYSTEM/INHIBITOR / proteasomal degradation / nitric oxide / inhibitor / IMMUNE SYSTEM / IMMUNE SYSTEM-INHIBITOR complex
Function / homology
Function and homology information


SCF ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular signal transduction / protein ubiquitination / cytosol
Similarity search - Function
SSB2, SOCS box domain / : / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / SPRY domain / B30.2/SPRY domain ...SSB2, SOCS box domain / : / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
INNN(ABU) Cyclic peptide inhibitor / SPRY domain-containing SOCS box protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.59 Å
AuthorsLaw, R.H.P. / Caradoc-Davies, T.T. / Norton, R.S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1099428 Australia
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: A Cyclic Peptide Inhibitor of the iNOS-SPSB Protein-Protein Interaction as a Potential Anti-Infective Agent.
Authors: Sadek, M.M. / Barlow, N. / Leung, E.W.W. / Williams-Noonan, B.J. / Yap, B.K. / Shariff, F.M. / Caradoc-Davies, T.T. / Nicholson, S.E. / Chalmers, D.K. / Thompson, P.E. / Law, R.H.P. / Norton, R.S.
History
DepositionJun 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPRY domain-containing SOCS box protein 2
B: INNN(ABU) cyclic peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)24,4082
Polymers24,4082
Non-polymers00
Water4,576254
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR and SPR
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-0 kcal/mol
Surface area9050 Å2
Unit cell
Length a, b, c (Å)41.040, 61.950, 84.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SPRY domain-containing SOCS box protein 2 / SSB-2 / Gene-rich cluster protein C9


Mass: 23849.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPSB2, GRCC9, SSB2 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: Q99619
#2: Protein/peptide INNN(ABU) cyclic peptide inhibitor


Type: Cyclic peptide / Class: Inhibitor / Mass: 558.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: INNN(ABU) Cyclic peptide inhibitor
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1M CHES, 20% PEG 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 29, 2017
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.59→42.5 Å / Num. obs: 29881 / % possible obs: 99.9 % / Redundancy: 11.3 % / Biso Wilson estimate: 18.42 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.024 / Net I/σ(I): 22.6
Reflection shellResolution: 1.59→1.68 Å / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 3.2 / Rpim(I) all: 0.241

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.59→42.46 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.086 / SU Rfree Blow DPI: 0.084 / SU Rfree Cruickshank DPI: 0.079
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1443 4.84 %RANDOM
Rwork0.174 ---
obs0.175 29823 100 %-
Displacement parametersBiso mean: 20.89 Å2
Baniso -1Baniso -2Baniso -3
1--4.3389 Å20 Å20 Å2
2--0.6836 Å20 Å2
3---3.6553 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: 1 / Resolution: 1.59→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1525 0 6 254 1785
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011608HARMONIC2
X-RAY DIFFRACTIONt_angle_deg12187HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d540SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes38HARMONIC2
X-RAY DIFFRACTIONt_gen_planes244HARMONIC5
X-RAY DIFFRACTIONt_it1608HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.14
X-RAY DIFFRACTIONt_other_torsion13.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion189SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2060SEMIHARMONIC4
LS refinement shellResolution: 1.59→1.65 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2294 142 4.95 %
Rwork0.1974 2727 -
all0.1991 2869 -
obs--99.48 %
Refinement TLS params.Method: refined / Origin x: 2.795 Å / Origin y: -0.5804 Å / Origin z: -8.968 Å
111213212223313233
T-0.0677 Å2-0.0127 Å2-0.0019 Å2--0.0565 Å2-0.0049 Å2---0.0538 Å2
L0.3993 °2-0.0134 °2-0.0346 °2-1.4062 °20.6628 °2--1.3076 °2
S0.0174 Å °0.0002 Å °-0.0482 Å °0.046 Å °0.0088 Å °-0.063 Å °0.0728 Å °0.0056 Å °-0.0262 Å °
Refinement TLS groupSelection details: { A|* }

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