[English] 日本語
Yorodumi
- PDB-3mgn: D-Peptide inhibitor PIE71 in complex with IQN17 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mgn
TitleD-Peptide inhibitor PIE71 in complex with IQN17
Components
  • D-PEPTIDE INHIBITOR PIE71
  • IQN17
KeywordsVIRAL PROTEIN/VIRAL PROTEIN inhibitor / PIE71 / IQN17 / HIV / helix / coiled-coil / D-peptide inhibitor / VIRAL PROTEIN-VIRAL PROTEIN inhibitor complex
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / D-PEPTIDE INHIBITOR PIE71
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHill, C.P. / Whitby, F.G. / Kay, M. / Francis, N.
CitationJournal: J.Virol. / Year: 2010
Title: Design of a potent D-peptide HIV-1 entry inhibitor with a strong barrier to resistance.
Authors: Welch, B.D. / Francis, J.N. / Redman, J.S. / Paul, S. / Weinstock, M.T. / Reeves, J.D. / Lie, Y.S. / Whitby, F.G. / Eckert, D.M. / Hill, C.P. / Root, M.J. / Kay, M.S.
History
DepositionApr 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IQN17
B: IQN17
C: IQN17
D: IQN17
E: IQN17
F: IQN17
G: D-PEPTIDE INHIBITOR PIE71
H: D-PEPTIDE INHIBITOR PIE71
I: D-PEPTIDE INHIBITOR PIE71
J: D-PEPTIDE INHIBITOR PIE71
K: D-PEPTIDE INHIBITOR PIE71
L: D-PEPTIDE INHIBITOR PIE71


Theoretical massNumber of molelcules
Total (without water)44,04512
Polymers44,04512
Non-polymers00
Water7,008389
1
A: IQN17
B: IQN17
C: IQN17
H: D-PEPTIDE INHIBITOR PIE71
K: D-PEPTIDE INHIBITOR PIE71
L: D-PEPTIDE INHIBITOR PIE71


Theoretical massNumber of molelcules
Total (without water)22,0226
Polymers22,0226
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-80 kcal/mol
Surface area11330 Å2
MethodPISA
2
D: IQN17
E: IQN17
F: IQN17
G: D-PEPTIDE INHIBITOR PIE71
I: D-PEPTIDE INHIBITOR PIE71
J: D-PEPTIDE INHIBITOR PIE71


Theoretical massNumber of molelcules
Total (without water)22,0226
Polymers22,0226
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-85 kcal/mol
Surface area11060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.920, 30.791, 132.802
Angle α, β, γ (deg.)90.000, 91.690, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide
IQN17


Mass: 5466.574 Da / Num. of mol.: 6 / Source method: obtained synthetically
#2: Protein/peptide
D-PEPTIDE INHIBITOR PIE71


Type: Cyclic peptide / Class: Inhibitor / Mass: 1874.236 Da / Num. of mol.: 6 / Source method: obtained synthetically / References: D-PEPTIDE INHIBITOR PIE71
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: QIAGEN PACT condition G4 - 20% Peg 3350, 0.1 M Bis Tris Propane, pH 7.5, 0.2 M Potassium Thiocyanate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 82774 / Num. obs: 82774 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.052 / Χ2: 0.954 / Net I/σ(I): 19.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.453.90.31681000.787197.6
1.45-1.513.90.15181340.995197.5
1.51-1.583.90.13681040.982196.9
1.58-1.6640.11980621.015196.6
1.66-1.764.40.10881011.052196.7
1.76-1.950.09282210.98197.7
1.9-2.0960.07483750.934199
2.09-2.397.40.06384170.9141100
2.39-3.027.50.04785210.8121100
3.02-3010.10.04887391.0551100

-
Phasing

Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.95 Å
Translation2.5 Å27.95 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→27.94 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.313 / WRfactor Rwork: 0.286 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.789 / SU B: 1.349 / SU ML: 0.056 / SU R Cruickshank DPI: 0.084 / SU Rfree: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1654 2 %RANDOM
Rwork0.261 ---
obs0.262 82186 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.03 Å2 / Biso mean: 31.168 Å2 / Biso min: 6.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å2-0.08 Å2
2--0.43 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.4→27.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 0 389 3383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223097
X-RAY DIFFRACTIONr_angle_refined_deg1.0942.0344047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3465323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.90825.769104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25615602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7311519
X-RAY DIFFRACTIONr_chiral_restr0.0660.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212037
X-RAY DIFFRACTIONr_mcbond_it0.6621.51797
X-RAY DIFFRACTIONr_mcangle_it1.12522831
X-RAY DIFFRACTIONr_scbond_it1.70831300
X-RAY DIFFRACTIONr_scangle_it2.8224.51216
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 126 -
Rwork0.306 5818 -
all-5944 -
obs--97.71 %

+
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