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- PDB-1znt: 18 NMR structures of AcAMP2-Like Peptide with non Natural Fluoroa... -

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Entry
Database: PDB / ID: 1znt
Title18 NMR structures of AcAMP2-Like Peptide with non Natural Fluoroaromatic Residue (AcAMP2F18Pff/Y20Pff) complex with N,N,N-triacetylchitotriose
ComponentsAMARANTHUS CAUDATUS ANTIMICROBIAL PEPTIDE 2
KeywordsANTIMICROBIAL PROTEIN / alfa-helix / anti-parallel beta-sheet
Function / homology
Function and homology information


chitin binding / defense response to fungus / killing of cells of another organism / defense response to bacterium
Similarity search - Function
Antimicrobial peptide, C6 type, conserved site / Plant C6 type antimicrobial peptide (AMP) signature. / Chitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily
Similarity search - Domain/homology
triacetyl-beta-chitotriose / Antimicrobial peptide 2
Similarity search - Component
MethodSOLUTION NMR / The structures are based on a total 314 cross peaks, 248 NOE-derived distance restraints, and finally 208 distance constraints, 18 come from cys-cys disulfide were used in the final round of calculation
AuthorsChavez, M.I. / Andreu, C. / Vidal, P. / Aboitiz, N. / Freire, F. / Groves, P. / Asensio, J.L. / Asensio, G. / Muraki, M. / Canada, F.J. / Jimenez-Barbero, J.
Citation
Journal: Chemistry / Year: 2005
Title: On the Importance of Carbohydrate-Aromatic Interactions for the Molecular Recognition of Oligosaccharides by Proteins: NMR Studies of the Structure and Binding Affinity of AcAMP2-like Peptides ...Title: On the Importance of Carbohydrate-Aromatic Interactions for the Molecular Recognition of Oligosaccharides by Proteins: NMR Studies of the Structure and Binding Affinity of AcAMP2-like Peptides with Non-Natural Naphthyl and Fluoroaromatic Residues
Authors: Chavez, M.I. / Andreu, C. / Vidal, P. / Aboitiz, N. / Freire, F. / Groves, P. / Asensio, J.L. / Asensio, G. / Muraki, M. / Canada, F.J. / Jimenez-Barbero, J.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: H NMR study of the solution structure of Ac-AMP2, a sugar binding antimicrobial protein isolated from Amaranthus caudatus
Authors: Martins, J.C. / Maes, D. / Loris, R. / Pepermans, H.A.M. / Wyns, L. / Willem, R. / Verheyden, P.
#2: Journal: Protein Pept.Lett. / Year: 2002
Title: The importance of CH/pi interactions to the function of carbohydrate binding proteins
Authors: Muraki, M.
#3: Journal: Chembiochem / Year: 2004
Title: NMR and modeling studies of protein-carbohydrate interactions: synthesis, three-dimensional structure, and recognition properties of a minimum hevein domain with binding affinity for chitooligosaccharides
Authors: Aboitiz, N. / Vila-Perello, M. / Groves, P. / Asensio, J.L. / Andreu, D. / Canada, F.J. / Jimenez-Barbero, J.
#4: Journal: Proteins / Year: 2000
Title: NMR investigations of protein-carbohydrate interactions: studies on the relevance of Trp/Tyr variations in lectin binding sites as deduced from titration microcalorimetry and NMR studies on ...Title: NMR investigations of protein-carbohydrate interactions: studies on the relevance of Trp/Tyr variations in lectin binding sites as deduced from titration microcalorimetry and NMR studies on hevein domains. Determination of the NMR structure of the complex between pseudohevein and N,N',N"-triacetylchitotriose
Authors: Asensio, J.L. / Siebert, H.C. / von Der Lieth, C.W. / Laynez, J. / Bruix, M. / Soedjanaamadja, U.M. / Beintema, J.J. / Canada, F.J. / Gabius, H.J. / Jimenez-Barbero, J.
#5: Journal: Chem.Biol. / Year: 2000
Title: Structural basis for chitin recognition by defense proteins: GlcNAc residues are bound in a multivalent fashion by extended binding sites in hevein domains
Authors: Asensio, J.L. / Canada, F.J. / Siebert, H.C. / Laynez, J. / Poveda, A. / Nieto, P.M. / Soedjanaamadja, U.M. / Gabius, H.J. / Jimenez-Barbero, J.
#6: Journal: Protein Eng. / Year: 2000
Title: Chemically prepared hevein domains: effect of C-terminal truncation and the mutagenesis of aromatic residues on the affinity for chitin
Authors: Muraki, M. / Morii, H. / Harata, K.
History
DepositionMay 12, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 2.1Mar 26, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMARANTHUS CAUDATUS ANTIMICROBIAL PEPTIDE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8402
Polymers3,2131
Non-polymers6281
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 30Fewest restraint violation, secondary lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide AMARANTHUS CAUDATUS ANTIMICROBIAL PEPTIDE 2 / ACMP2


Mass: 3212.771 Da / Num. of mol.: 1 / Mutation: Phe18PFF, Tyr20PFF / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in AMARANTHUS CAUDATUS (INCA-WHEAT). SEQUENCE PREPARED BY STANDARD SOLID PHASE PEPTIDE SYNTHESIS ...Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in AMARANTHUS CAUDATUS (INCA-WHEAT). SEQUENCE PREPARED BY STANDARD SOLID PHASE PEPTIDE SYNTHESIS PROTOCOLS USING FMOC CHEMISTRY. Phe18 and Tyr20 have been mutated to the non proteinogenic aminoacid 4-fluorophenyalanine.
References: UniProt: P27275*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques which are NOESY at tm=300 and TOCSY at tm=50 and 70 ms

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Sample preparation

DetailsContents: 1mM AcAMP2F18Pff/Y20Pff, 12mM chitotriose, 20mM Phosphate buffer; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 5.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.2Brukercollection
XEASY1.3.13Wuthrichdata analysis
DYANA1.5Guentertstructure solution
Amber5Kollmanrefinement
RefinementMethod: The structures are based on a total 314 cross peaks, 248 NOE-derived distance restraints, and finally 208 distance constraints, 18 come from cys-cys disulfide were used in the final round of calculation
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: Fewest restraint violation, secondary lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 18

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