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- PDB-2sec: STRUCTURAL COMPARISON OF TWO SERINE PROTEINASE-PROTEIN INHIBITOR ... -

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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/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 ...: / 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/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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.

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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.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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