[English] 日本語
Yorodumi
- PDB-3own: Potent macrocyclic renin inhibitors -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3own
TitlePotent macrocyclic renin inhibitors
ComponentsRenin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / RENIN / PROTEASE / ASPARTYL PROTEASE / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


renin / juxtaglomerular apparatus development / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / amyloid-beta metabolic process / angiotensin maturation ...renin / juxtaglomerular apparatus development / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / amyloid-beta metabolic process / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / cell maturation / response to cAMP / insulin-like growth factor receptor binding / hormone-mediated signaling pathway / kidney development / regulation of blood pressure / male gonad development / cellular response to xenobiotic stimulus / apical part of cell / peptidase activity / response to lipopolysaccharide / aspartic-type endopeptidase activity / signaling receptor binding / proteolysis / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-3OW / Chem-3OX / ACETATE ION / Renin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBorkakoti, N. / Derbyshire, D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Design and synthesis of potent macrocyclic renin inhibitors.
Authors: Sund, C. / Belda, O. / Wiktelius, D. / Sahlberg, C. / Vrang, L. / Sedig, S. / Hamelink, E. / Henderson, I. / Agback, T. / Jansson, K. / Borkakoti, N. / Derbyshire, D. / Eneroth, A. / Samuelsson, B.
History
DepositionSep 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Renin
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4199
Polymers74,8102
Non-polymers1,6097
Water6,179343
1
A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3217
Polymers37,4051
Non-polymers9166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0982
Polymers37,4051
Non-polymers6931
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Renin
hetero molecules

A: Renin
hetero molecules

A: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,96321
Polymers112,2153
Non-polymers2,74818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6410 Å2
ΔGint-79 kcal/mol
Surface area38390 Å2
MethodPISA
4
B: Renin
hetero molecules

B: Renin
hetero molecules

B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,2946
Polymers112,2153
Non-polymers2,0793
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area4200 Å2
ΔGint-33 kcal/mol
Surface area38660 Å2
MethodPISA
5
A: Renin
B: Renin
hetero molecules

A: Renin
B: Renin
hetero molecules

A: Renin
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,25727
Polymers224,4316
Non-polymers4,82721
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area16810 Å2
ΔGint-117 kcal/mol
Surface area70860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.827, 141.827, 141.827
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-802-

NA

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Renin / Angiotensinogenase


Mass: 37405.152 Da / Num. of mol.: 2 / Fragment: UNP residues 67-406 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00797, renin

-
Non-polymers , 5 types, 350 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-3OX / (2S,4S)-4-hydroxy-2-(1-methylethyl)-4-[(4R,13S)-18-[methyl(methylsulfonyl)amino]-2,15-dioxo-4-phenyl-11-oxa-3,14-diazatricyclo[14.3.1.1~5,9~]henicosa-1(20),5(21),6,8,16,18-hexaen-13-yl]-N-(2-methylpropyl)butanamide


Mass: 692.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H48N4O7S
#5: Chemical ChemComp-3OW / (2S,4S)-4-hydroxy-2-(1-methylethyl)-4-[(4S,13S)-18-[methyl(methylsulfonyl)amino]-2,15-dioxo-4-phenyl-11-oxa-3,14-diazatricyclo[14.3.1.1~5,9~]henicosa-1(20),5(21),6,8,16,18-hexaen-13-yl]-N-(2-methylpropyl)butanamide


Mass: 692.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H48N4O7S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 3.18 Å3/Da / Density % sol: 61.29 %
Crystal growTemperature: 299 K / Method: vapor diffusion / Details: vapor diffusion, temperature 299K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→70.913 Å / Num. all: 64051 / Num. obs: 64051 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.115.50.5311.45101892810.531100
2.11-2.245.40.4161.74776887960.416100
2.24-2.395.40.2742.54516683150.274100
2.39-2.585.60.1813.94308377050.181100
2.58-2.835.60.1444.53989871310.144100
2.83-3.165.60.1155.43580564450.115100
3.16-3.655.50.1045.93150457460.104100
3.65-4.475.30.115.42589248430.1199.9
4.47-6.325.20.0975.71943737610.09799.1
6.32-70.9135.40.0826.71086420280.08293.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→70.89 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 4.043 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 3227 5.1 %RANDOM
Rwork0.2168 ---
obs0.2187 63618 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.05 Å2 / Biso mean: 24.5479 Å2 / Biso min: 3 Å2
Refinement stepCycle: LAST / Resolution: 2→70.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5148 0 112 343 5603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225392
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.9787320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8965664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24424.091220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46615854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.131520
X-RAY DIFFRACTIONr_chiral_restr0.1290.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024088
X-RAY DIFFRACTIONr_nbd_refined0.220.22441
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23605
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2372
X-RAY DIFFRACTIONr_metal_ion_refined0.030.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.210
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0850.22
X-RAY DIFFRACTIONr_mcbond_it1.1221.53310
X-RAY DIFFRACTIONr_mcangle_it2.03225338
X-RAY DIFFRACTIONr_scbond_it3.20932117
X-RAY DIFFRACTIONr_scangle_it4.9134.51982
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 234 -
Rwork0.283 4484 -
all-4718 -
obs--100 %

+
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://pdbjlc1.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