[English] 日本語
Yorodumi
- PDB-8q0w: Endothiapepsin in complex with ligand (3R,5R)-3-(2-((allyl(methyl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8q0w
TitleEndothiapepsin in complex with ligand (3R,5R)-3-(2-((allyl(methyl)amino)methyl)thiazol-4-yl)-5-(3-(4-(trifluoromethyl)phenyl)-1,2,4-oxadiazol-5-yl)pyrrolidin-3-ol (CBWS-SE-086)
ComponentsEndothiapepsin
KeywordsHYDROLASE / Endothiapepsin / ligand complex
Function / homology
Function and homology information


endothiapepsin / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Aspergillopepsin-like catalytic domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
ACETATE ION / : / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsMueller, J.M. / Eckelt, S. / Klebe, G. / Glinca, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structures of Endothiapepsin with ligands derived from merged fragment hits
Authors: Mueller, J.M.
History
DepositionJul 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7298
Polymers33,8141
Non-polymers9157
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint12 kcal/mol
Surface area12650 Å2
Unit cell
Length a, b, c (Å)44.891, 72.757, 52.461
Angle α, β, γ (deg.)90.000, 109.140, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Endothiapepsin / Aspartate protease


Mass: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-IJG / (3~{R},5~{R})-3-[2-[[methyl(prop-2-enyl)amino]methyl]-1,3-thiazol-4-yl]-5-[3-[4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl]pyrrolidin-3-ol


Mass: 465.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H22F3N5O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Protein at 5 mg/mL in 100 mM ammoniumacetate pH 4.6, reservoir: 100 mM ammoniumacetate, 100 mM sodium acetate pH 4.6, 24 % PEG4000, 292 K, 2+2 yL drops over 1 mL reservoir, streak seeding

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.99187 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 51792 / % possible obs: 98.7 % / Redundancy: 3.73 % / Biso Wilson estimate: 16.71 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.23
Reflection shellResolution: 1.49→1.58 Å / Redundancy: 3.62 % / Mean I/σ(I) obs: 2 / Num. unique obs: 7907 / CC1/2: 0.869 / % possible all: 93.7

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→34.5 Å / SU ML: 0.1562 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.8646
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1841 2589 5 %
Rwork0.1607 49185 -
obs0.1619 51774 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.01 Å2
Refinement stepCycle: LAST / Resolution: 1.49→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 56 209 2634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752541
X-RAY DIFFRACTIONf_angle_d1.06843497
X-RAY DIFFRACTIONf_chiral_restr0.0851410
X-RAY DIFFRACTIONf_plane_restr0.0062447
X-RAY DIFFRACTIONf_dihedral_angle_d11.619816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.29941190.27582264X-RAY DIFFRACTION82.09
1.52-1.550.27281460.22492774X-RAY DIFFRACTION99.83
1.55-1.580.21291440.19852729X-RAY DIFFRACTION99.72
1.58-1.620.21681430.18372732X-RAY DIFFRACTION99.9
1.62-1.660.21971460.1722765X-RAY DIFFRACTION99.66
1.66-1.70.2141440.17092734X-RAY DIFFRACTION99.79
1.7-1.750.20621450.1692754X-RAY DIFFRACTION99.9
1.75-1.810.17111460.16662776X-RAY DIFFRACTION99.97
1.81-1.870.20891460.16372767X-RAY DIFFRACTION99.97
1.87-1.950.17091450.152757X-RAY DIFFRACTION99.79
1.95-2.040.1661450.13942768X-RAY DIFFRACTION99.69
2.04-2.140.15191440.14122727X-RAY DIFFRACTION99.69
2.14-2.280.15881450.14262758X-RAY DIFFRACTION99.83
2.28-2.450.19141450.15292748X-RAY DIFFRACTION99.93
2.45-2.70.19671450.15892772X-RAY DIFFRACTION99.83
2.7-3.090.16681460.16872772X-RAY DIFFRACTION99.83
3.09-3.890.19581450.15882747X-RAY DIFFRACTION98.87
3.89-34.50.16891500.1582841X-RAY DIFFRACTION99.83
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)
18.08969523689-1.416048624324.207916970282.1548497374-0.4722933738273.492724837860.0700140014621-0.0632649911736-0.299675985052-0.1033026118060.01744930632670.01067668798190.07417589821720.0913431751525-0.07039542196630.1314247178020.001833908622270.02156688747890.1308526141050.007084639234440.1177844802319.40526196893-12.54020987225.57499267981
24.108466810610.9461978831680.06701456750095.46668567191-0.1219533855226.11134922798-0.1420043390350.1522990655370.0414035030579-0.1679104727580.1115575357370.489786554846-0.115547219697-0.4100322032450.00431784382980.14604262405-0.0146891540094-0.01378182693850.1596527049310.00570311545490.19252786135-6.11826135161-6.009275264490.973765655099
31.84105640522-0.4338544790890.7129941095911.81520266854-1.117867499173.13132464635-0.0337804574729-0.0239481709344-0.01671519575330.0667160333486-0.0286868183928-0.01517699641420.147901486825-0.007021600449640.07374944433060.160945933332-0.008445335810120.01615593238270.136313874606-0.01231530713210.1363547809053.89948891493-13.712151634415.1844616857
41.315614256390.605065875603-0.4606247220751.18543314048-0.2119881758271.36441204829-0.0174707584358-0.0591809789392-0.04043061270230.0292240426154-0.02276904161520.0141616729727-0.0377876830726-0.1259795554440.04356004644510.1361212240970.01760172283190.00531947432950.156615198442-0.004178842900360.1543383695042.08767286028-3.3019738210617.1165358927
54.939562886320.04193003392783.906684958876.73242177605-3.039430625256.70987744225-0.0225411889584-0.8258332170710.3273059165660.3624459133820.03626081607430.804553390689-0.327301771572-0.994442330667-0.02649017939040.1549490198360.02376559236650.05961073977160.31209573436-0.03715734797780.243568289248-11.3204942881-5.2951261727224.6153638334
61.566184437260.430135978371-1.023121234543.671943488960.667641101491.782243334060.00881293919916-0.340512431665-0.214224038274-0.00316309601665-0.02967433068360.401269766470.00448536951305-0.2795282211690.007242532941090.143943509728-0.02453102692820.01848364894410.203146224694-0.007924489899140.171927102116-5.62501207826-11.765816399820.6520060923
73.265021890120.9721540147890.3719114640754.281257665730.8936569634711.812113610350.0271936774394-0.288399222197-0.1098187922520.427004971076-0.0823309535013-0.07613404557650.105125542518-0.3037126570060.06573289710.238780915687-0.002749201350950.02680351743880.1992721358030.005397318985010.1330689763926.22953755227-14.989674394629.7022748599
83.57435754322-2.09416234438-0.8444205063577.84448309320.2224979920420.229760437269-0.201152583061-0.39029697250.2038342615980.5334295267540.1753454625230.012017514812-0.095958461397-0.07780407830870.01650922191450.211832019230.01897184112110.0008519607962530.193668632552-0.02659113817410.1337816584397.46246221828-1.9976692643733.48245768
94.870615549310.4816500199061.909969364425.52393974126-0.6504878591787.44252034937-0.193273900864-0.1388753270480.372379162432-0.09635705274630.2579119409650.215724227983-0.368275318317-0.190242149351-0.03150431280860.167761501640.0534018709547-0.005603181836680.17885461582-0.0184511984380.1687794340530.1698328621454.2590081201120.9725812466
100.3726968496080.0361063436129-0.09524402974630.5453680600990.1332721061031.26742607169-0.0245649591975-0.06343249910080.01115879697790.01766824117960.0002307019880360.00983384446044-0.0277581018498-0.006783800687010.02573372911290.1340481179940.00777279452615-0.005586004655780.123372267189-0.0022556162590.1503186487098.75107190122-4.4853124237512.4571058827
111.63786033411-0.246178693540.5295560394930.532870664611-0.1133685567920.6540222659220.004623848487490.0265765758640.0197473159532-0.0115558805655-0.0319319936305-0.0644538777941-0.02781520674090.01013686790860.03361036844380.136816159685-0.0006511316783460.01824892369930.116924871698-0.001738135318910.137946000342.401747814577.01550984971-5.28049136229
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 9 )1 - 91 - 9
22chain 'A' and (resid 10 through 16 )10 - 1610 - 16
33chain 'A' and (resid 17 through 32 )17 - 3217 - 32
44chain 'A' and (resid 33 through 47 )33 - 4733 - 47
55chain 'A' and (resid 48 through 52 )48 - 5248 - 52
66chain 'A' and (resid 53 through 60 )53 - 6053 - 60
77chain 'A' and (resid 61 through 68 )61 - 6861 - 68
88chain 'A' and (resid 69 through 73 )69 - 7369 - 73
99chain 'A' and (resid 74 through 79 )74 - 7974 - 79
1010chain 'A' and (resid 82 through 183 )82 - 18382 - 183
1111chain 'A' and (resid 184 through 330 )184 - 330184 - 330

+
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