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- PDB-1bcr: COMPLEX OF THE WHEAT SERINE CARBOXYPEPTIDASE, CPDW-II, WITH THE M... -

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Basic information

Entry
Database: PDB / ID: 1bcr
TitleCOMPLEX OF THE WHEAT SERINE CARBOXYPEPTIDASE, CPDW-II, WITH THE MICROBIAL PEPTIDE ALDEHYDE INHIBITOR, ANTIPAIN, AND ARGININE AT ROOM TEMPERATURE
Components
  • (SERINE CARBOXYPEPTIDASE ...) x 2
  • ANTIPAIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / MICROBIAL PEPTIDE ALDEHYDE INHIBITOR / SERINE PROTEASE-INHIBITOR COMPLEX / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


carboxypeptidase D / serine-type carboxypeptidase activity / proteolysis
Similarity search - Function
Rossmann fold - #11320 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #940 / Serine carboxypeptidase, serine active site / Serine carboxypeptidases, serine active site. / Peptidase S10, serine carboxypeptidase / Serine carboxypeptidases, histidine active site / Serine carboxypeptidase / Serine carboxypeptidases, histidine active site. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular ...Rossmann fold - #11320 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #940 / Serine carboxypeptidase, serine active site / Serine carboxypeptidases, serine active site. / Peptidase S10, serine carboxypeptidase / Serine carboxypeptidases, histidine active site / Serine carboxypeptidase / Serine carboxypeptidases, histidine active site. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Antipain / ARGININE / Serine carboxypeptidase 2
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
Actinobacteria (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBullock, T.L. / Remington, S.J.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Peptide aldehyde complexes with wheat serine carboxypeptidase II: implications for the catalytic mechanism and substrate specificity.
Authors: Bullock, T.L. / Breddam, K. / Remington, S.J.
#1: Journal: Biochemistry / Year: 1994
Title: Structure of the Complex of L-Benzylsuccinate with Wheat Serine Carboxypeptidase at 2.0 Angstrom Resolution
Authors: Bullock, T.L. / Branchaud, B. / Remington, S.J.
#2: Journal: Biochemistry / Year: 1992
Title: Refined Atomic Model of Wheat Serine Carboxypeptidase II at 2.2 Angstrom Resolution
Authors: Liao, D.I. / Breddam, K. / Sweet, R.M. / Bullock, T. / Remington, S.J.
History
DepositionNov 3, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 28, 2011Group: Non-polymer description / Structure summary
Revision 1.4Sep 5, 2012Group: Derived calculations
Revision 1.5Dec 12, 2012Group: Other
Revision 1.6Jun 5, 2013Group: Atomic model
Revision 2.0May 15, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Polymer sequence
Category: database_PDB_caveat / entity_poly ...database_PDB_caveat / entity_poly / pdbx_database_status / pdbx_distant_solvent_atoms / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 4.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE CARBOXYPEPTIDASE II
B: SERINE CARBOXYPEPTIDASE II
C: ANTIPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1757
Polymers47,7833
Non-polymers1,3914
Water3,459192
1
A: SERINE CARBOXYPEPTIDASE II
B: SERINE CARBOXYPEPTIDASE II
C: ANTIPAIN
hetero molecules

A: SERINE CARBOXYPEPTIDASE II
B: SERINE CARBOXYPEPTIDASE II
C: ANTIPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,34914
Polymers95,5666
Non-polymers2,7838
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)98.400, 98.400, 209.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: CIS PROLINE - PRO A 43 / 2: CIS PROLINE - PRO A 54 / 3: CIS PROLINE - PRO A 96

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Components

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SERINE CARBOXYPEPTIDASE ... , 2 types, 2 molecules AB

#1: Protein SERINE CARBOXYPEPTIDASE II


Mass: 29180.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / Tissue: WHEAT GERM / References: UniProt: P08819, carboxypeptidase D
#2: Protein SERINE CARBOXYPEPTIDASE II


Mass: 17995.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / Tissue: WHEAT GERM / References: UniProt: P08819, carboxypeptidase D

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide ANTIPAIN


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 607.725 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Actinobacteria (bacteria) / References: Antipain

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Sugars , 3 types, 3 molecules

#4: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-6-deoxy-Altp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-ManpNAc]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 193 molecules

#7: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.31 Å3/Da / Density % sol: 76.82 %
Crystal grow
*PLUS
pH: 4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mM1dropNaCl
20.2 %(w/v)PEG40001drop
350 mMsodium acetate1drop
41.25 Msodium chloride1reservoir
550 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceWavelength: 1.54
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRedundancy: 2.23 % / Rmerge(I) obs: 0.054
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 29444 / % possible obs: 86 % / Num. measured all: 65638 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 71 %

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Processing

Software
NameClassification
R-AXISdata collection
TNTrefinement
R-AXISdata reduction
RefinementResolution: 2.5→21 Å / σ(F): 0 /
RfactorNum. reflection
obs0.162 29444
Refinement stepCycle: LAST / Resolution: 2.5→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 0 92 192 3489
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.53
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.019
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_plane_restr0.020.019

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