[English] 日本語
Yorodumi
- PDB-6qeo: Crystal structure of Porcine Pancreatic Elastase (PPE) in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qeo
TitleCrystal structure of Porcine Pancreatic Elastase (PPE) in complex with the 3-Oxo-beta-Sultam inhibitor LMC269
ComponentsChymotrypsin-like elastase family member 1
KeywordsHYDROLASE / Serine Hydrolases / Pancreatic Porcine Elastase / Inhibitor / 3-Oxo-beta-Sultams / Sulfonylation
Function / homology
Function and homology information


pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-J02 / PHOSPHATE ION / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBrito, J.A. / Almeida, V.T. / Carvalho, L.M. / Moreira, R. / Archer, M.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: 3-Oxo-beta-sultam as a Sulfonylating Chemotype for Inhibition of Serine Hydrolases and Activity-Based Protein Profiling.
Authors: Carvalho, L.A.R. / Almeida, V.T. / Brito, J.A. / Lum, K.M. / Oliveira, T.F. / Guedes, R.C. / Goncalves, L.M. / Lucas, S.D. / Cravatt, B.F. / Archer, M. / Moreira, R.
History
DepositionJan 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chymotrypsin-like elastase family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6446
Polymers25,9291
Non-polymers7145
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-23 kcal/mol
Surface area10540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.740, 57.714, 74.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Chymotrypsin-like elastase family member 1 / Elastase-1


Mass: 25929.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase

-
Non-polymers , 5 types, 227 molecules

#2: Chemical ChemComp-J02 / 2-methyl-1-[[1-[(4-nitrophenyl)methyl]-1,2,3-triazol-4-yl]methylamino]-1-oxidanylidene-propane-2-sulfonic acid


Mass: 383.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N5O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.9 / Details: 70 % (V/V) MPD 10 mM KP pH 5.9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 1.3→33.94 Å / Num. obs: 49091 / % possible obs: 91.8 % / Redundancy: 4.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.024 / Net I/σ(I): 13.4
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.65 / Num. unique obs: 2456 / CC1/2: 0.63 / Rpim(I) all: 0.44 / % possible all: 52

-
Processing

Software
NameVersionClassification
XDS20180409data reduction
Aimless0.7.1data scaling
STARANISO1.10.15data scaling
PHASERphasing
BUSTER-TNTrefinement
PHENIX(1.13_2992)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YM9

4ym9


Resolution: 1.3→33.94 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.89
RfactorNum. reflection% reflection
Rfree0.1674 2414 4.91 %
Rwork0.1301 --
obs0.1319 49091 87.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→33.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 44 222 2088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091979
X-RAY DIFFRACTIONf_angle_d1.1722722
X-RAY DIFFRACTIONf_dihedral_angle_d13.882696
X-RAY DIFFRACTIONf_chiral_restr0.087301
X-RAY DIFFRACTIONf_plane_restr0.006352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.289-1.31530.2607410.2155765X-RAY DIFFRACTION25
1.3153-1.34390.2492640.20781494X-RAY DIFFRACTION48
1.3439-1.37510.23791190.19012056X-RAY DIFFRACTION67
1.3751-1.40950.24981340.1762481X-RAY DIFFRACTION80
1.4095-1.44760.19941550.15712812X-RAY DIFFRACTION91
1.4476-1.49020.19971420.14313019X-RAY DIFFRACTION98
1.4902-1.53830.19021430.12683125X-RAY DIFFRACTION100
1.5383-1.59330.17661610.11613075X-RAY DIFFRACTION99
1.5933-1.65710.16461470.1163094X-RAY DIFFRACTION99
1.6571-1.73250.17461630.11983093X-RAY DIFFRACTION99
1.7325-1.82390.17861630.12163102X-RAY DIFFRACTION99
1.8239-1.93810.15211640.11833090X-RAY DIFFRACTION99
1.9381-2.08770.17341630.11583093X-RAY DIFFRACTION99
2.0877-2.29780.1411790.11093119X-RAY DIFFRACTION99
2.2978-2.63020.15151490.12343016X-RAY DIFFRACTION94
2.6302-3.31330.17251960.13373136X-RAY DIFFRACTION99
3.3133-33.95290.15441310.13973228X-RAY DIFFRACTION95

+
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://pdbjlvh1.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