[English] 日本語
Yorodumi
- PDB-2sec: STRUCTURAL COMPARISON OF TWO SERINE PROTEINASE-PROTEIN INHIBITOR ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2sec
TitleSTRUCTURAL COMPARISON OF TWO SERINE PROTEINASE-PROTEIN INHIBITOR COMPLEXES. EGLIN-C-SUBTILISIN CARLSBERG AND CI-2-SUBTILISIN NOVO
Components
  • EGLIN C
  • SUBTILISIN CARLSBERG
KeywordsCOMPLEX(SERINE PROTEINASE-INHIBITOR)
Function / homology
Function and homology information


subtilisin / serine-type endopeptidase inhibitor activity / response to wounding / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily ...Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / : / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Subtilisin Carlsberg / Eglin C
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsMcphalen, C.A. / James, M.N.G.
Citation
Journal: Biochemistry / Year: 1988
Title: Structural comparison of two serine proteinase-protein inhibitor complexes: eglin-c-subtilisin Carlsberg and CI-2-subtilisin Novo.
Authors: McPhalen, C.A. / James, M.N.
#1: Journal: FEBS Lett. / Year: 1985
Title: Crystal and Molecular Structure of the Inhibitor Eglin from Leeches in Complex with Subtilisin Carlsberg
Authors: Mcphalen, C.A. / Schnebli, H.P. / James, M.N.G.
History
DepositionSep 5, 1988Processing site: BNL
SupersessionSep 7, 1988ID: 1SEC
Revision 1.0Sep 7, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE CROSS-OVER CONNECTION BETWEEN STRANDS 1 AND 2 OF SHEET S1E IS LEFT-HANDED. THE BETA-SHEET ...SHEET THE CROSS-OVER CONNECTION BETWEEN STRANDS 1 AND 2 OF SHEET S1E IS LEFT-HANDED. THE BETA-SHEET OF THE INHIBITOR IS IRREGULAR, WITH WELL-ORDERED WATER MOLECULES PROVIDING ALL HYDROGEN-BONDING BRIDGES BETWEEN STRANDS 2 AND 3. SEE THE REFERENCE CITED ON THE *JRNL* RECORDS ABOVE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: SUBTILISIN CARLSBERG
I: EGLIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5255
Polymers35,4052
Non-polymers1203
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-29 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.310, 41.410, 56.500
Angle α, β, γ (deg.)69.51, 83.67, 75.32
Int Tables number1
Space group name H-MP1
Atom site foot note1: RESIDUE PRO E 168 IS A CIS PROLINE. / 2: RESIDUE THR E 211 IS A CIS THREONINE.

-
Components

#1: Protein SUBTILISIN CARLSBERG


Mass: 27306.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / References: UniProt: P00780, subtilisin
#2: Protein EGLIN C


Mass: 8099.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Production host: unidentified (others) / References: UniProt: P01051
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSUBTILISIN HAS BEEN ASSIGNED CHAIN IDENTIFIER *E* AND EGLIN C HAS BEEN ASSIGNED CHAIN IDENTIFIER ...SUBTILISIN HAS BEEN ASSIGNED CHAIN IDENTIFIER *E* AND EGLIN C HAS BEEN ASSIGNED CHAIN IDENTIFIER *I*. THE AMINO ACID SEQUENCE NUMBERING USED FOR EGLIN C IS BASED ON A SEQUENCE ALIGNMENT WITH CHYMOTRYPSIN INHIBITOR 2 (CI-2) AND USES THE CI-2 NUMBERING SCHEME. THE STRUCTURE OF SUBTILISIN CARLSBERG WAS REFINED ON THE BASIS OF THE PUBLISHED AMINO ACID SEQUENCE OF THE PROTEIN (E.L.SMITH ET AL., J. BIOL. CHEM., V. 243, P. 2184, 1968). THE DNA SEQUENCE OF A CARLSBERG-LIKE ENZYME FROM BACILLUS LICHENIFORMIS (JACOBS ET AL., NUCLEIC ACIDS RES., V. 13, P. 8913, 1985) DIFFERS FROM THE ORIGINAL AMINO ACID SEQUENCE OF SUBTILISIN CARLSBERG AT FIVE POSITIONS - SMITH JACOBS SER E 103 THR E 103 ALA E 129 PRO E 129 ASN E 158 SER E 158 SER E 161 ASN E 161 ASN E 212 SER E 212 THE ELECTRON DENSITY AT POSITION 158 COULD BE CONSISTENT WITH THE DNA SEQUENCE. THE DENSITY AT THE OTHER FOUR POSITIONS IS CONSISTENT WITH THE RESULTS OF THE PROTEIN SEQUENCING.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal
*PLUS
Density % sol: 44 %
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion, hanging drop
Details: McPhalen, C.A., (1985) Proc. Natl. Acad. Sci. USA., 82, 7242.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.4 Mammonium sulfate1reservoir
250 mM1reservoirKH2PO4

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→8 Å / σ(I): 1 /
RfactorNum. reflection
obs0.136 27094
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 3 170 2623
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.008
X-RAY DIFFRACTIONp_angle_d0.0270.016
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.016
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0170.012
X-RAY DIFFRACTIONp_chiral_restr0.1460.08
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.136
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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