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- PDB-1gac: NMR structure of asymmetric homodimer of a82846b, a glycopeptide ... -

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Basic information

Entry
Database: PDB / ID: 1gac
TitleNMR structure of asymmetric homodimer of a82846b, a glycopeptide antibiotic, complexed with its cell wall pentapeptide fragment
Components
  • CELL WALL PENTAPEPTIDE
  • CHLOROORIENTICIN A
KeywordsPEPTIDE/ANTIBIOTIC / PEPTIDE-ANTIBIOTIC COMPLEX / CELL WALL PEPTIDE / GLYCOPEPTIDE / ANTIBIOTIC / VANCOMYCIN PEPTIDE-ANTIBIOTIC COMPLEX
Function / homologyChloroorienticin A / vancosamine / :
Function and homology information
Biological speciesAMYCOLATOPSIS ORIENTALIS (bacteria)
MethodSOLUTION NMR
AuthorsKline, A.D. / Prowse, W.G. / Skelton, M.A. / Loncharich, R.J.
CitationJournal: Biochemistry / Year: 1995
Title: Conformation of A82846B, a Glycopeptide Antibiotic, Complexed with its Cell Wall Fragment: An Asymmetric Homodimer Determined Using NMR Spectroscopy.
Authors: Prowse, W.G. / Kline, A.D. / Skelton, M.A. / Loncharich, R.J.
History
DepositionMay 24, 1995Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_poly / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_polymer_linkage / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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 3.0Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELL WALL PENTAPEPTIDE
B: CELL WALL PENTAPEPTIDE
C: CHLOROORIENTICIN A
D: CHLOROORIENTICIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2488
Polymers3,2794
Non-polymers9694
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint5 kcal/mol
Surface area2330 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)80 / 80
Representative

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Components

#1: Protein/peptide CELL WALL PENTAPEPTIDE


Mass: 489.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) AMYCOLATOPSIS ORIENTALIS (bacteria)
#2: Protein/peptide CHLOROORIENTICIN A / A82846B / A82846 FACTOR B / CHLOROEREMOMYCIN


Type: Glycopeptide / Class: Antibiotic / Mass: 1149.977 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: CHLOROORIENTICIN A IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY ONE DISACCHARIDE ON RESIDUE 4 AND ONE MONOSACCHARIDE ON RESIDUE 6.
Source: (synth.) AMYCOLATOPSIS ORIENTALIS (bacteria) / References: NOR: NOR00687, Chloroorienticin A
#3: Polysaccharide vancosamine-(1-2)-beta-D-glucopyranose


Type: oligosaccharide, Glycopeptide / Class: Antibiotic / Mass: 323.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CHLOROORIENTICIN A IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY ONE DISACCHARIDE ON RESIDUE 4 AND ONE MONOSACCHARIDE ON RESIDUE 6.
References: Chloroorienticin A
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5][ad621m-1a_1-5_3*C_3*N]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(2+1)][a-L-2,6-deoxy-Glcp3N]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-RER / vancosamine / (1R,3S,4S,5S)-3-amino-2,3,6-trideoxy-3-methyl-alpha-L-arabino-hexopyranose


Type: L-saccharide, alpha linking, Glycopeptide / Class: Antibiotic / Mass: 161.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H15NO3
Details: CHLOROORIENTICIN A IS A TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY ONE DISACCHARIDE ON RESIDUE 4 AND ONE MONOSACCHARIDE ON RESIDUE 6.
References: Chloroorienticin A / Comment: antibiotic*YM
Compound detailsCHLOROORIENTICIN A IS A TRICYCLIC GLYCOPEPTIDE, A MEMBER OF THE VANCOMYCIN FAMILY. THE SCAFFOLD IS ...CHLOROORIENTICIN A IS A TRICYCLIC GLYCOPEPTIDE, A MEMBER OF THE VANCOMYCIN FAMILY. THE SCAFFOLD IS A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS FURTHER GLYCOSYLATED BY ONE DISACCHARIDE AND ONE MONOSACCHARIDE HERE, CHLOROORIENTICIN A IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND THE THREE LIGANDS (HET) BGC AND TWO RER.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: CONCENTRATION = 5 MM

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Sample preparation

Sample conditionspH: 5.0 / Temperature: 273.65 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR softwareName: CHARMM
Developer: BROOKS,BRUCCOLERI,OLAFSON,STATES,SWAMINATHAN, KARPLUS
Classification: refinement
NMR ensembleConformers calculated total number: 80 / Conformers submitted total number: 80

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