[English] 日本語
Yorodumi
- PDB-6d3x: Highly Potent and Selective Plasmin Inhibitors Based on the Sunfl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d3x
TitleHighly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma
Components
  • Plasminogen
  • Trypsin inhibitor 1
KeywordsHYDROLASE / Protease / SFTI / complex
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / protein antigen binding / mononuclear cell migration / negative regulation of endopeptidase activity / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / tissue regeneration / protein antigen binding / mononuclear cell migration / negative regulation of endopeptidase activity / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / myoblast differentiation / negative regulation of cell-substrate adhesion / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / endopeptidase inhibitor activity / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / serine-type endopeptidase inhibitor activity / Schaffer collateral - CA1 synapse / kinase binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / protease binding / collagen-containing extracellular matrix / endopeptidase activity / blood microparticle / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, plasmin / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily ...Peptidase S1A, plasmin / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / 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 family, serine active site. / Serine proteases, trypsin domain profile. / 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
Plasminogen / Trypsin inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Helianthus annuus (common sunflower)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsLaw, R.H.P. / Wu, G.
CitationJournal: J. Med. Chem. / Year: 2019
Title: Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma.
Authors: Swedberg, J.E. / Wu, G. / Mahatmanto, T. / Durek, T. / Caradoc-Davies, T.T. / Whisstock, J.C. / Law, R.H.P. / Craik, D.J.
History
DepositionApr 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Plasminogen
B: Plasminogen
C: Trypsin inhibitor 1
D: Trypsin inhibitor 1


Theoretical massNumber of molelcules
Total (without water)57,2464
Polymers57,2464
Non-polymers00
Water5,729318
1
A: Plasminogen
C: Trypsin inhibitor 1


Theoretical massNumber of molelcules
Total (without water)28,6232
Polymers28,6232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-6 kcal/mol
Surface area10700 Å2
MethodPISA
2
B: Plasminogen
D: Trypsin inhibitor 1


Theoretical massNumber of molelcules
Total (without water)28,6232
Polymers28,6232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-6 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.728, 80.127, 83.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Plasminogen / microplasmin


Mass: 27009.055 Da / Num. of mol.: 2 / Fragment: UNP residues 565-810
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLG / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P00747, plasmin
#2: Protein/peptide Trypsin inhibitor 1 / SFTI-1


Mass: 1613.921 Da / Num. of mol.: 2 / Fragment: UNP residues 40-53 / Mutation: T4Y, I7K / Source method: obtained synthetically / Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 21% PEG4000, 0.1 M magnesium chloride, 0.1 M sodium citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→57.724 Å / Num. obs: 49556 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 15.37 Å2 / Rpim(I) all: 0.068 / Rrim(I) all: 0.198 / Rsym value: 0.185 / Net I/av σ(I): 3.4 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.8-1.98.21.140.671570.4161.2141.14100
1.9-2.018.20.7140.967430.260.7610.714100
2.01-2.158.20.4671.563680.170.4970.467100
2.15-2.328.20.3282.159340.120.350.328100
2.32-2.558.20.2442.954990.0890.260.244100
2.55-2.858.20.1713.949610.0630.1820.171100
2.85-3.298.10.1244.944340.0460.1330.124100
3.29-4.0280.0856.637600.0310.0910.085100
4.02-5.697.90.0569.429730.0210.060.056100
5.69-46.5527.60.0549.717270.0210.0580.05499.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 5UGG & 1SFI

5ugg

1sfi


Resolution: 1.8→46.552 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.22
RfactorNum. reflection% reflection
Rfree0.2161 2468 5 %
Rwork0.1888 --
obs0.1902 49405 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.74 Å2 / Biso mean: 20.8373 Å2 / Biso min: 7.79 Å2
Refinement stepCycle: final / Resolution: 1.8→46.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3894 0 0 327 4221
Biso mean---28.96 -
Num. residues----516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.83470.30341440.277325822726
1.8347-1.87210.29161260.246525692695
1.8721-1.91280.26081390.231625792718
1.9128-1.95730.24571380.225125522690
1.9573-2.00630.27321450.207725822727
2.0063-2.06050.25851240.201925722696
2.0605-2.12110.22121150.192826152730
2.1211-2.18960.22171350.189125702705
2.1896-2.26790.24961170.186426042721
2.2679-2.35860.22451670.183325622729
2.3586-2.4660.23011420.182725822724
2.466-2.5960.19951410.185626042745
2.596-2.75860.24571510.182625882739
2.7586-2.97160.21711370.180226292766
2.9716-3.27060.1861100.179526322742
3.2706-3.74360.18321440.166426532797
3.7436-4.71590.17341580.16126502808
4.7159-46.56730.20041350.197528122947
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)
14.9655-0.69090.40634.4582-1.04431.2964-0.0487-0.01230.09070.04270.04990.3341-0.0979-0.269-0.14370.08630.00320.01460.1725-0.00150.1492-31.9215-6.100729.0649
23.1312-1.5234-1.24982.69991.20983.4494-0.0178-0.0001-0.3316-0.04070.0724-0.08540.3513-0.1047-0.00670.144-0.0136-0.01240.08260.0220.16-22.8512-13.673723.6003
33.45130.3645-0.81221.6057-0.32642.8935-0.09010.1266-0.3415-0.09040.0943-0.0570.23640.073-0.00190.16610.0087-0.010.1377-0.01020.1501-16.4459-12.419917.7727
41.84930.3435-0.14620.4896-0.34721.32010.03320.00110.15660.007-0.00180.0814-0.0186-0.0056-0.03310.12940.0049-0.00090.1133-0.00770.1305-20.1276-4.081725.0053
51.56011.25960.24741.88680.56131.54660.0777-0.28160.12340.047-0.02390.0725-0.05620.0711-0.03450.11160.00060.00340.1947-0.02070.1139-13.55540.727238.6203
61.64440.6163-0.58431.70040.28543.22040.0599-0.03310.12990.0232-0.03630.0483-0.0280.11410.01950.1057-0.00550.00340.0985-0.01490.1087-18.5717-0.66433.5927
72.02090.3117-0.70251.8343-0.06634.488-0.01840.27520.1586-0.1779-0.04290.009-0.31010.0168-0.02040.1088-0.0104-0.00380.11230.01060.1071-14.15314.089618.4011
83.8210.3598-0.58463.91260.03630.0937-0.10070.23050.1281-0.04810.0547-0.4952-0.12610.4206-0.02180.11750.0018-0.00240.23580.03060.179531.8468-6.526422.078
92.2133-0.7591-0.30860.9123-0.25172.45-0.0286-0.1163-0.2310.04520.09560.06870.1228-0.0699-0.04110.11950.0043-0.00430.09430.01870.122718.8907-13.020931.199
103.4671-2.05021.00091.7478-0.48231.7421-0.1454-0.2524-0.14430.20950.14430.108-0.0323-0.0397-0.00090.1398-0.01080.00820.16810.02590.11913.4234-6.545837.5695
111.6514-0.95890.20231.0122-0.09381.79020.10210.22520.1469-0.085-0.0833-0.1296-0.06470.0552-0.00770.1099-0.01870.02170.16760.02930.123322.4168-2.897519.923
121.2469-0.97710.19831.5138-0.71282.20520.09820.2830.0275-0.1052-0.03980.00860.0004-0.0395-0.03570.1248-0.00490.00920.17470.02750.103714.8945-0.734815.425
131.6137-0.2129-0.40831.52240.10275.4704-0.1016-0.19810.20470.13770.0089-0.0386-0.4590.18950.09440.09990.001-0.00860.1095-0.02170.098714.3234.069533.1379
148.4111-2.74952.24971.6043-0.08777.17970.0475-0.36290.17980.2963-0.2902-0.405-0.0960.51930.10470.141-0.0121-0.02640.21820.05690.2296-4.3335-9.438233.6677
152.74261.72521.87421.64980.8077.50030.18340.24480.1962-0.0582-0.22090.5623-0.0417-0.39390.04850.1418-0.0275-0.00880.2284-0.03520.27814.3928-9.790918.1849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 546 through 567 )A546 - 567
2X-RAY DIFFRACTION2chain 'A' and (resid 568 through 585 )A568 - 585
3X-RAY DIFFRACTION3chain 'A' and (resid 586 through 640 )A586 - 640
4X-RAY DIFFRACTION4chain 'A' and (resid 641 through 697 )A641 - 697
5X-RAY DIFFRACTION5chain 'A' and (resid 698 through 743 )A698 - 743
6X-RAY DIFFRACTION6chain 'A' and (resid 744 through 771 )A744 - 771
7X-RAY DIFFRACTION7chain 'A' and (resid 772 through 791 )A772 - 791
8X-RAY DIFFRACTION8chain 'B' and (resid 546 through 567 )B546 - 567
9X-RAY DIFFRACTION9chain 'B' and (resid 568 through 630 )B568 - 630
10X-RAY DIFFRACTION10chain 'B' and (resid 631 through 657 )B631 - 657
11X-RAY DIFFRACTION11chain 'B' and (resid 658 through 710 )B658 - 710
12X-RAY DIFFRACTION12chain 'B' and (resid 711 through 771 )B711 - 771
13X-RAY DIFFRACTION13chain 'B' and (resid 772 through 791 )B772 - 791
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 14 )C1 - 14
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 14 )D1 - 14

+
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