data_3VFK # _entry.id 3VFK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.329 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3VFK RCSB RCSB069982 WWPDB D_1000069982 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1JW4 'Native MBP structure used for molecular replacement' unspecified PDB 3RUN 'same crystallographic strategy: vancomycin bound to a T4 lysozyme-substrate fusion' unspecified PDB 3RUL 'same crystallographic strategy: dalbavancin bound to the same ubiquitin fusion' unspecified PDB 3RUM 'same crystallographic strategy: ristocetin bound to a MBP-substrate fusion' unspecified PDB 3VFJ 'The structure of monodechloro-teicoplanin in complex with its ligand, using MBP as a ligand' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3VFK _pdbx_database_status.recvd_initial_deposition_date 2012-01-09 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Economou, N.J.' 1 'Weeks, S.D.' 2 'Grasty, K.C.' 3 'Loll, P.J.' 4 # _citation.id primary _citation.title 'Structure of the complex between teicoplanin and a bacterial cell-wall peptide: use of a carrier-protein approach.' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 69 _citation.page_first 520 _citation.page_last 533 _citation.year 2013 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23519660 _citation.pdbx_database_id_DOI 10.1107/S0907444912050469 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Economou, N.J.' 1 ? primary 'Zentner, I.J.' 2 ? primary 'Lazo, E.' 3 ? primary 'Jakoncic, J.' 4 ? primary 'Stojanoff, V.' 5 ? primary 'Weeks, S.D.' 6 ? primary 'Grasty, K.C.' 7 ? primary 'Cocklin, S.' 8 ? primary 'Loll, P.J.' 9 ? # _cell.entry_id 3VFK _cell.length_a 88.010 _cell.length_b 25.180 _cell.length_c 38.710 _cell.angle_alpha 90.00 _cell.angle_beta 109.18 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3VFK _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'ubiquitin, C-terminal fused by Cys-Lys-D-Ala-D-Ala' 8952.293 1 ? ? ? ? 2 polymer nat 'MonodeChloro- Teicoplanin A2-2' 1172.539 1 ? ? ? ? 3 non-polymer man 2-amino-2-deoxy-beta-D-glucopyranose 179.171 1 ? ? ? ? 4 non-polymer syn '8-METHYLNONANOIC ACID' 172.265 1 ? ? ? ? 5 non-polymer man 2-acetamido-2-deoxy-beta-D-glucopyranose 221.208 1 ? ? ? ? 6 non-polymer man alpha-D-mannopyranose 180.156 1 ? ? ? ? 7 water nat water 18.015 10 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name Ubiquitin # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(D)' no yes ;MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG(CCS) K(DAL)(DAL) ; MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGCKAA A ? 2 'polypeptide(L)' no yes '(GHP)(3MY)(3FG)(GHP)(GHP)(OMX)(3FG)' GYXGGYX G ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 GLN n 1 3 ILE n 1 4 PHE n 1 5 VAL n 1 6 LYS n 1 7 THR n 1 8 LEU n 1 9 THR n 1 10 GLY n 1 11 LYS n 1 12 THR n 1 13 ILE n 1 14 THR n 1 15 LEU n 1 16 GLU n 1 17 VAL n 1 18 GLU n 1 19 PRO n 1 20 SER n 1 21 ASP n 1 22 THR n 1 23 ILE n 1 24 GLU n 1 25 ASN n 1 26 VAL n 1 27 LYS n 1 28 ALA n 1 29 LYS n 1 30 ILE n 1 31 GLN n 1 32 ASP n 1 33 LYS n 1 34 GLU n 1 35 GLY n 1 36 ILE n 1 37 PRO n 1 38 PRO n 1 39 ASP n 1 40 GLN n 1 41 GLN n 1 42 ARG n 1 43 LEU n 1 44 ILE n 1 45 PHE n 1 46 ALA n 1 47 GLY n 1 48 LYS n 1 49 GLN n 1 50 LEU n 1 51 GLU n 1 52 ASP n 1 53 GLY n 1 54 ARG n 1 55 THR n 1 56 LEU n 1 57 SER n 1 58 ASP n 1 59 TYR n 1 60 ASN n 1 61 ILE n 1 62 GLN n 1 63 LYS n 1 64 GLU n 1 65 SER n 1 66 THR n 1 67 LEU n 1 68 HIS n 1 69 LEU n 1 70 VAL n 1 71 LEU n 1 72 ARG n 1 73 LEU n 1 74 ARG n 1 75 GLY n 1 76 CCS n 1 77 LYS n 1 78 DAL n 1 79 DAL n 2 1 GHP n 2 2 3MY n 2 3 3FG n 2 4 GHP n 2 5 GHP n 2 6 OMX n 2 7 3FG n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene UBC _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details 'four C-terminal amino acids added non-recombinantly with native chemical ligation' _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _entity_src_nat.entity_id 2 _entity_src_nat.pdbx_src_id 1 _entity_src_nat.pdbx_alt_source_flag sample _entity_src_nat.pdbx_beg_seq_num ? _entity_src_nat.pdbx_end_seq_num ? _entity_src_nat.common_name ? _entity_src_nat.pdbx_organism_scientific 'Actinoplanes teichomyceticus' _entity_src_nat.pdbx_ncbi_taxonomy_id 1867 _entity_src_nat.genus ? _entity_src_nat.species ? _entity_src_nat.strain ? _entity_src_nat.tissue ? _entity_src_nat.tissue_fraction ? _entity_src_nat.pdbx_secretion ? _entity_src_nat.pdbx_fragment ? _entity_src_nat.pdbx_variant ? _entity_src_nat.pdbx_cell_line ? _entity_src_nat.pdbx_atcc ? _entity_src_nat.pdbx_cellular_location ? _entity_src_nat.pdbx_organ ? _entity_src_nat.pdbx_organelle ? _entity_src_nat.pdbx_cell ? _entity_src_nat.pdbx_plasmid_name ? _entity_src_nat.pdbx_plasmid_details ? _entity_src_nat.details ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 UNP UBC_HUMAN P0CG48 1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG 1 ? 2 PDB 3VFK 3VFK 2 ? ? ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3VFK A 1 ? 75 ? P0CG48 1 ? 75 ? 1 75 2 2 3VFK G 1 ? 7 ? 3VFK 1 ? 7 ? 1 7 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 3VFK CCS A 76 ? UNP P0CG48 ? ? 'SEE REMARK 999' 76 1 1 3VFK LYS A 77 ? UNP P0CG48 ? ? 'SEE REMARK 999' 77 2 1 3VFK DAL A 78 ? UNP P0CG48 ? ? 'SEE REMARK 999' 78 3 1 3VFK DAL A 79 ? UNP P0CG48 ? ? 'SEE REMARK 999' 79 4 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight 3FG 'L-peptide linking' . '(2S)-amino(3,5-dihydroxyphenyl)ethanoic acid' ? 'C8 H9 N O4' 183.161 3MY 'D-peptide linking' n 3-chloro-D-tyrosine ? 'C9 H10 Cl N O3' 215.634 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CCS 'L-peptide linking' n 'CARBOXYMETHYLATED CYSTEINE' ? 'C5 H9 N O4 S' 179.194 DAL 'D-peptide linking' . D-ALANINE ? 'C3 H7 N O2' 89.093 GCS 'D-saccharide, beta linking' . 2-amino-2-deoxy-beta-D-glucopyranose 2-AMINO-2-DEOXY-D-GLUCOSE 'C6 H13 N O5' 179.171 GHP 'D-peptide linking' . '(2R)-amino(4-hydroxyphenyl)ethanoic acid' ? 'C8 H9 N O3' 167.162 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MAN 'D-saccharide, alpha linking' . alpha-D-mannopyranose ? 'C6 H12 O6' 180.156 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 NAG 'D-saccharide, beta linking' . 2-acetamido-2-deoxy-beta-D-glucopyranose ? 'C8 H15 N O6' 221.208 OMX 'L-peptide linking' n '(betaR)-beta-hydroxy-L-Tyrosine' ? 'C9 H11 N O4' 197.188 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 T55 non-polymer . '8-METHYLNONANOIC ACID' ? 'C10 H20 O2' 172.265 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3VFK _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.00 _exptl_crystal.density_percent_sol 38.42 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4.6 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '0.1 M magnesium chloride, 0.1 M sodium acetate 4.6, 18% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 291K' # _diffrn.id 1 _diffrn.ambient_temp 93 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2009-04-10 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Cryogenically-cooled single crystal Si(111)side bounce monochromator' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9792 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 24-ID-E' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 24-ID-E _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9792 # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 3VFK _reflns.observed_criterion_sigma_I -3 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 19.294 _reflns.d_resolution_high 2.8 _reflns.number_obs 2084 _reflns.number_all ? _reflns.percent_possible_obs 99.2 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3VFK _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 2084 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.04 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 19.294 _refine.ls_d_res_high 2.800 _refine.ls_percent_reflns_obs 99.95 _refine.ls_R_factor_obs 0.2789 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2776 _refine.ls_R_factor_R_free 0.3057 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.46 _refine.ls_number_reflns_R_free 93 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] 8.4159 _refine.aniso_B[2][2] -20.2601 _refine.aniso_B[3][3] 11.8442 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] -18.7315 _refine.aniso_B[2][3] -0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.424 _refine.solvent_model_param_bsol 77.331 _refine.pdbx_solvent_vdw_probe_radii 0.30 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.00 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 'PDB entry 1UBQ' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.45 _refine.pdbx_overall_phase_error 34.93 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 711 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 47 _refine_hist.number_atoms_solvent 10 _refine_hist.number_atoms_total 768 _refine_hist.d_res_high 2.800 _refine_hist.d_res_low 19.294 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 0.005 ? ? 777 'X-RAY DIFFRACTION' ? f_angle_d 0.847 ? ? 1061 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 12.765 ? ? 318 'X-RAY DIFFRACTION' ? f_chiral_restr 0.037 ? ? 122 'X-RAY DIFFRACTION' ? f_plane_restr 0.004 ? ? 132 'X-RAY DIFFRACTION' ? # _struct.entry_id 3VFK _struct.title 'The structure of monodechloro-teicoplanin in complex with its ligand, using ubiquitin as a ligand carrier' _struct.pdbx_descriptor 'ubiquitin, C-terminal fused by Cys-Lys-D-Ala-D-Ala, teicoplanin' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3VFK _struct_keywords.pdbx_keywords 'SUGAR BINDING PROTEIN/ANTIBIOTIC' _struct_keywords.text 'teicoplanin, acetylation of cyteine with iodoacetate modification, SUGAR BINDING PROTEIN-ANTIBIOTIC complex' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 5 ? F N N 6 ? G N N 7 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 THR A 22 ? GLU A 34 ? THR A 22 GLU A 34 1 ? 13 HELX_P HELX_P2 2 PRO A 37 ? ASP A 39 ? PRO A 37 ASP A 39 5 ? 3 HELX_P HELX_P3 3 LEU A 56 ? ASN A 60 ? LEU A 56 ASN A 60 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A GLY 75 C ? ? ? 1_555 A CCS 76 N ? ? A GLY 75 A CCS 76 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale2 covale both ? A CCS 76 C ? ? ? 1_555 A LYS 77 N ? ? A CCS 76 A LYS 77 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale3 covale both ? A LYS 77 C ? ? ? 1_555 A DAL 78 N ? ? A LYS 77 A DAL 78 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale4 covale both ? A DAL 78 C ? ? ? 1_555 A DAL 79 N ? ? A DAL 78 A DAL 79 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale5 covale both ? B GHP 1 C ? ? ? 1_555 B 3MY 2 N ? ? G GHP 1 G 3MY 2 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale6 covale none ? B GHP 1 C5 ? ? ? 1_555 B 3FG 3 OD1 ? ? G GHP 1 G 3FG 3 1_555 ? ? ? ? ? ? ? 1.362 ? ? covale7 covale both ? B 3MY 2 C ? ? ? 1_555 B 3FG 3 N ? ? G 3MY 2 G 3FG 3 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale8 covale none ? B 3MY 2 OBD ? ? ? 1_555 B GHP 4 C3 ? ? G 3MY 2 G GHP 4 1_555 ? ? ? ? ? ? ? 1.383 ? ? covale9 covale both ? B 3FG 3 C ? ? ? 1_555 B GHP 4 N ? ? G 3FG 3 G GHP 4 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale10 covale both ? B GHP 4 C ? ? ? 1_555 B GHP 5 N ? ? G GHP 4 G GHP 5 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale11 covale none ? B GHP 4 C5 ? ? ? 1_555 B OMX 6 OH ? ? G GHP 4 G OMX 6 1_555 ? ? ? ? ? ? ? 1.384 ? ? covale12 covale one ? B GHP 4 O4 ? ? ? 1_555 C GCS . C1 ? ? G GHP 4 G GCS 8 1_555 ? ? ? ? ? ? ? 1.383 ? ? covale13 covale both ? B GHP 5 C ? ? ? 1_555 B OMX 6 N ? ? G GHP 5 G OMX 6 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale14 covale none ? B GHP 5 C3 ? ? ? 1_555 B 3FG 7 CG1 ? ? G GHP 5 G 3FG 7 1_555 ? ? ? ? ? ? ? 1.399 ? ? covale15 covale both ? B OMX 6 C ? ? ? 1_555 B 3FG 7 N ? ? G OMX 6 G 3FG 7 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale16 covale one ? B OMX 6 OC ? ? ? 1_555 E NAG . C1 ? ? G OMX 6 G NAG 10 1_555 ? ? ? ? ? ? ? 1.384 ? ? covale17 covale one ? B 3FG 7 OD1 ? ? ? 1_555 F MAN . C1 ? ? G 3FG 7 G MAN 11 1_555 ? ? ? ? ? ? ? 1.422 ? ? covale18 covale both ? C GCS . N2 ? ? ? 1_555 D T55 . C ? ? G GCS 8 G T55 9 1_555 ? ? ? ? ? ? ? 1.462 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id GHP _struct_mon_prot_cis.label_seq_id 5 _struct_mon_prot_cis.label_asym_id B _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id GHP _struct_mon_prot_cis.auth_seq_id 5 _struct_mon_prot_cis.auth_asym_id G _struct_mon_prot_cis.pdbx_label_comp_id_2 OMX _struct_mon_prot_cis.pdbx_label_seq_id_2 6 _struct_mon_prot_cis.pdbx_label_asym_id_2 B _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 OMX _struct_mon_prot_cis.pdbx_auth_seq_id_2 6 _struct_mon_prot_cis.pdbx_auth_asym_id_2 G _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle 1.18 # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 5 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 ILE A 13 ? GLU A 16 ? ILE A 13 GLU A 16 A 2 GLN A 2 ? THR A 7 ? GLN A 2 THR A 7 A 3 SER A 65 ? LEU A 71 ? SER A 65 LEU A 71 A 4 GLN A 41 ? PHE A 45 ? GLN A 41 PHE A 45 A 5 LYS A 48 ? GLN A 49 ? LYS A 48 GLN A 49 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 O LEU A 15 ? O LEU A 15 N ILE A 3 ? N ILE A 3 A 2 3 N PHE A 4 ? N PHE A 4 O LEU A 67 ? O LEU A 67 A 3 4 O HIS A 68 ? O HIS A 68 N ILE A 44 ? N ILE A 44 A 4 5 N PHE A 45 ? N PHE A 45 O LYS A 48 ? O LYS A 48 # _database_PDB_matrix.entry_id 3VFK _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 3VFK _atom_sites.fract_transf_matrix[1][1] 0.011362 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.003952 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.039714 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.027351 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C CL N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 MET 1 1 1 MET MET A . n A 1 2 GLN 2 2 2 GLN GLN A . n A 1 3 ILE 3 3 3 ILE ILE A . n A 1 4 PHE 4 4 4 PHE PHE A . n A 1 5 VAL 5 5 5 VAL VAL A . n A 1 6 LYS 6 6 6 LYS LYS A . n A 1 7 THR 7 7 7 THR THR A . n A 1 8 LEU 8 8 8 LEU LEU A . n A 1 9 THR 9 9 9 THR THR A . n A 1 10 GLY 10 10 10 GLY GLY A . n A 1 11 LYS 11 11 11 LYS LYS A . n A 1 12 THR 12 12 12 THR THR A . n A 1 13 ILE 13 13 13 ILE ILE A . n A 1 14 THR 14 14 14 THR THR A . n A 1 15 LEU 15 15 15 LEU LEU A . n A 1 16 GLU 16 16 16 GLU GLU A . n A 1 17 VAL 17 17 17 VAL VAL A . n A 1 18 GLU 18 18 18 GLU GLU A . n A 1 19 PRO 19 19 19 PRO PRO A . n A 1 20 SER 20 20 20 SER SER A . n A 1 21 ASP 21 21 21 ASP ASP A . n A 1 22 THR 22 22 22 THR THR A . n A 1 23 ILE 23 23 23 ILE ILE A . n A 1 24 GLU 24 24 24 GLU GLU A . n A 1 25 ASN 25 25 25 ASN ASN A . n A 1 26 VAL 26 26 26 VAL VAL A . n A 1 27 LYS 27 27 27 LYS LYS A . n A 1 28 ALA 28 28 28 ALA ALA A . n A 1 29 LYS 29 29 29 LYS LYS A . n A 1 30 ILE 30 30 30 ILE ILE A . n A 1 31 GLN 31 31 31 GLN GLN A . n A 1 32 ASP 32 32 32 ASP ASP A . n A 1 33 LYS 33 33 33 LYS LYS A . n A 1 34 GLU 34 34 34 GLU GLU A . n A 1 35 GLY 35 35 35 GLY GLY A . n A 1 36 ILE 36 36 36 ILE ILE A . n A 1 37 PRO 37 37 37 PRO PRO A . n A 1 38 PRO 38 38 38 PRO PRO A . n A 1 39 ASP 39 39 39 ASP ASP A . n A 1 40 GLN 40 40 40 GLN GLN A . n A 1 41 GLN 41 41 41 GLN GLN A . n A 1 42 ARG 42 42 42 ARG ARG A . n A 1 43 LEU 43 43 43 LEU LEU A . n A 1 44 ILE 44 44 44 ILE ILE A . n A 1 45 PHE 45 45 45 PHE PHE A . n A 1 46 ALA 46 46 46 ALA ALA A . n A 1 47 GLY 47 47 47 GLY GLY A . n A 1 48 LYS 48 48 48 LYS LYS A . n A 1 49 GLN 49 49 49 GLN GLN A . n A 1 50 LEU 50 50 50 LEU LEU A . n A 1 51 GLU 51 51 51 GLU GLU A . n A 1 52 ASP 52 52 52 ASP ASP A . n A 1 53 GLY 53 53 53 GLY GLY A . n A 1 54 ARG 54 54 54 ARG ARG A . n A 1 55 THR 55 55 55 THR THR A . n A 1 56 LEU 56 56 56 LEU LEU A . n A 1 57 SER 57 57 57 SER SER A . n A 1 58 ASP 58 58 58 ASP ASP A . n A 1 59 TYR 59 59 59 TYR TYR A . n A 1 60 ASN 60 60 60 ASN ASN A . n A 1 61 ILE 61 61 61 ILE ILE A . n A 1 62 GLN 62 62 62 GLN GLN A . n A 1 63 LYS 63 63 63 LYS LYS A . n A 1 64 GLU 64 64 64 GLU GLU A . n A 1 65 SER 65 65 65 SER SER A . n A 1 66 THR 66 66 66 THR THR A . n A 1 67 LEU 67 67 67 LEU LEU A . n A 1 68 HIS 68 68 68 HIS HIS A . n A 1 69 LEU 69 69 69 LEU LEU A . n A 1 70 VAL 70 70 70 VAL VAL A . n A 1 71 LEU 71 71 71 LEU LEU A . n A 1 72 ARG 72 72 72 ARG ARG A . n A 1 73 LEU 73 73 73 LEU LEU A . n A 1 74 ARG 74 74 74 ARG ARG A . n A 1 75 GLY 75 75 75 GLY GLY A . n A 1 76 CCS 76 76 76 CCS CCS A . n A 1 77 LYS 77 77 77 LYS LYS A . n A 1 78 DAL 78 78 78 DAL DAL A . n A 1 79 DAL 79 79 79 DAL DAL A . n B 2 1 GHP 1 1 1 GHP NTR G . n B 2 2 3MY 2 2 2 3MY 3MY G . n B 2 3 3FG 3 3 3 3FG 3FG G . n B 2 4 GHP 4 4 4 GHP GHP G . n B 2 5 GHP 5 5 5 GHP GHP G . n B 2 6 OMX 6 6 6 OMX OMX G . n B 2 7 3FG 7 7 7 3FG 3FG G . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 GCS 1 8 8 GCS GCS G . D 4 T55 1 9 9 T55 T55 G . E 5 NAG 1 10 10 NAG NAG G . F 6 MAN 1 11 11 MAN MAN G . G 7 HOH 1 201 1 HOH HOH A . G 7 HOH 2 202 2 HOH HOH A . G 7 HOH 3 203 3 HOH HOH A . G 7 HOH 4 204 4 HOH HOH A . G 7 HOH 5 205 5 HOH HOH A . G 7 HOH 6 206 6 HOH HOH A . G 7 HOH 7 207 7 HOH HOH A . G 7 HOH 8 208 8 HOH HOH A . G 7 HOH 9 209 9 HOH HOH A . G 7 HOH 10 210 10 HOH HOH A . # _pdbx_molecule_features.prd_id PRD_000882 _pdbx_molecule_features.name 'MonodeChloro- Teicoplanin A2-2' _pdbx_molecule_features.type Glycopeptide _pdbx_molecule_features.class Antibiotic _pdbx_molecule_features.details ? # loop_ _pdbx_molecule.instance_id _pdbx_molecule.prd_id _pdbx_molecule.asym_id 1 PRD_000882 B 1 PRD_000882 C 1 PRD_000882 D 1 PRD_000882 E 1 PRD_000882 F # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2013-01-09 2 'Structure model' 1 1 2013-03-27 3 'Structure model' 1 2 2013-04-03 4 'Structure model' 1 3 2013-06-19 5 'Structure model' 2 0 2020-07-29 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 5 'Structure model' repository Remediation 'Carbohydrate remediation' ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Structure summary' 2 3 'Structure model' 'Derived calculations' 3 4 'Structure model' 'Database references' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Derived calculations' 6 5 'Structure model' 'Polymer sequence' 7 5 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 5 'Structure model' chem_comp 2 5 'Structure model' entity 3 5 'Structure model' entity_poly 4 5 'Structure model' pdbx_chem_comp_identifier 5 5 'Structure model' pdbx_entity_nonpoly 6 5 'Structure model' struct_conn 7 5 'Structure model' struct_site 8 5 'Structure model' struct_site_gen # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_chem_comp.name' 2 5 'Structure model' '_chem_comp.type' 3 5 'Structure model' '_entity.pdbx_description' 4 5 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can' 5 5 'Structure model' '_pdbx_entity_nonpoly.name' 6 5 'Structure model' '_struct_conn.pdbx_dist_value' 7 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 8 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 9 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 10 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 11 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 12 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 13 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 14 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 15 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 16 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 17 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 18 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MOLREP phasing . ? 1 PHENIX refinement '(phenix.refine: 1.6.2_432)' ? 2 XDS 'data reduction' . ? 3 XSCALE 'data scaling' . ? 4 # _pdbx_entry_details.entry_id 3VFK _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details 'C-TERMINAL FUSED BY MODIFIED CYS-LYS-D-ALA-D-ALA' _pdbx_entry_details.compound_details ;AUTHORS STATED THE FOLLOWING: THE STARTING MATERIAL HAD TEICOPLANIN A2-2 THAT CONTAINED TWO CHLORINE ATOMS. THE ACTUAL CRYSTALS CONTAINED BOTH CHLORINE ATOMS BEFORE THEY WERE EXPOSED TO X-RAYS. ONE CHLORINE WAS REMOVED FROM TEICOPLANIN BY X-IRRADIATION DAMAGE EARLY IN THE DIFFRACTION EXPERIMENT TEICOPLANIN IS A FAMILY OF TETRACYCLIC GLYCOPEPTIDE ANTIBIOTICS. THE SCAFFOLD IS A HEPTAPEPTIDE FURTHER GLYCOSYLATED BY THREE MONO SACCHARIDES: MANNOSE, N-ACETYLGLUCOSAMINE AND BETA-D-GLUCOSAMINE AND ONLY DIFFER BY THE SIDE CHAIN ATTACHED TO THE LATTER. TEICOPLANIN A2-2 HAS 8-METHYLNONANOIC ACID ATTACHED TO GLUCOSAMINE. HERE, TEICOPLANIN A2-2 WAS UNDER RADIATION DAMAGE, WHICH CAUSES THE LOSS OF ONE CHLORINE ATOM. ; _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest ? # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ARG A 54 ? ? -175.15 127.86 2 1 3FG G 3 ? ? -143.02 -67.54 # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier GCS 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpNb GCS 'COMMON NAME' GMML 1.0 b-D-glucopyranosamine GCS 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpN GCS 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcN MAN 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DManpa MAN 'COMMON NAME' GMML 1.0 a-D-mannopyranose MAN 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-Manp MAN 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Man NAG 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpNAcb NAG 'COMMON NAME' GMML 1.0 N-acetyl-b-D-glucopyranosamine NAG 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpNAc NAG 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcNAc # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 2-amino-2-deoxy-beta-D-glucopyranose GCS 4 '8-METHYLNONANOIC ACID' T55 5 2-acetamido-2-deoxy-beta-D-glucopyranose NAG 6 alpha-D-mannopyranose MAN 7 water HOH #