data_1DFN # _entry.id 1DFN # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.287 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1DFN WWPDB D_1000172771 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1DFN _pdbx_database_status.recvd_initial_deposition_date 1991-01-18 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hill, C.P.' 1 'Yee, J.' 2 'Selsted, M.E.' 3 'Eisenberg, D.' 4 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Crystal structure of defensin HNP-3, an amphiphilic dimer: mechanisms of membrane permeabilization.' Science 251 1481 1485 1991 SCIEAS US 0036-8075 0038 ? 2006422 ? 1 'Primary Structures of Three Human Neutrophil Defensins' J.Clin.Invest. 76 1436 ? 1985 JCINAO US 0021-9738 0797 ? ? ? 2 'Defensins. Natural Peptide Antibiotics of Human Neutrophils' J.Clin.Invest. 76 1427 ? 1985 JCINAO US 0021-9738 0797 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Hill, C.P.' 1 primary 'Yee, J.' 2 primary 'Selsted, M.E.' 3 primary 'Eisenberg, D.' 4 1 'Selsted, M.E.' 5 1 'Harwig, S.S.L.' 6 1 'Ganz, T.' 7 1 'Schilling, J.W.' 8 1 'Lehrer, R.I.' 9 2 'Ganz, T.' 10 2 'Selsted, M.E.' 11 2 'Szklarek, D.' 12 2 'Harwig, S.S.L.' 13 2 'Daher, K.' 14 2 'Bainton, D.F.' 15 2 'Lehrer, R.I.' 16 # _cell.entry_id 1DFN _cell.length_a 30.800 _cell.length_b 45.000 _cell.length_c 40.300 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DFN _symmetry.space_group_name_H-M 'P 21 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 # 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 'DEFENSIN HNP-3' 3496.121 2 ? ? ? ? 2 water nat water 18.015 44 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code DCYCRIPACIAGERRYGTCIYQGRLWAFCC _entity_poly.pdbx_seq_one_letter_code_can DCYCRIPACIAGERRYGTCIYQGRLWAFCC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ASP n 1 2 CYS n 1 3 TYR n 1 4 CYS n 1 5 ARG n 1 6 ILE n 1 7 PRO n 1 8 ALA n 1 9 CYS n 1 10 ILE n 1 11 ALA n 1 12 GLY n 1 13 GLU n 1 14 ARG n 1 15 ARG n 1 16 TYR n 1 17 GLY n 1 18 THR n 1 19 CYS n 1 20 ILE n 1 21 TYR n 1 22 GLN n 1 23 GLY n 1 24 ARG n 1 25 LEU n 1 26 TRP n 1 27 ALA n 1 28 PHE n 1 29 CYS n 1 30 CYS 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 Homo _entity_src_gen.pdbx_gene_src_gene ? _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 ? _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 ? _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ? _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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code DEF1_HUMAN _struct_ref.entity_id 1 _struct_ref.pdbx_db_accession P59665 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code ;MRTLAILAAILLVALQAQAEPLQARADEVAAAPEQIAADIPEVVVSLAWDESLAPKHPGSRKNMACYCRIPACIAGERRY GTCIYQGRLWAFCC ; _struct_ref.pdbx_db_isoform ? # 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 1DFN A 2 ? 30 ? P59665 66 ? 94 ? 3 31 2 1 1DFN B 2 ? 30 ? P59665 66 ? 94 ? 3 31 # 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 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 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 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 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 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 # _exptl.entry_id 1DFN _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.00 _exptl_crystal.density_percent_sol 38.39 _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _refine.entry_id 1DFN _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.0 _refine.ls_d_res_high 1.9 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.19 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _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 ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _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_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 470 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 44 _refine_hist.number_atoms_total 514 _refine_hist.d_res_high 1.9 _refine_hist.d_res_low 10.0 # 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 p_bond_d 0.019 0.020 ? ? 'X-RAY DIFFRACTION' ? p_angle_d 0.049 0.040 ? ? 'X-RAY DIFFRACTION' ? p_angle_deg ? ? ? ? 'X-RAY DIFFRACTION' ? p_planar_d 0.045 0.050 ? ? 'X-RAY DIFFRACTION' ? p_hb_or_metal_coord ? ? ? ? 'X-RAY DIFFRACTION' ? p_mcbond_it 0.991 1.000 ? ? 'X-RAY DIFFRACTION' ? p_mcangle_it 1.720 1.500 ? ? 'X-RAY DIFFRACTION' ? p_scbond_it 1.565 1.000 ? ? 'X-RAY DIFFRACTION' ? p_scangle_it 2.427 1.500 ? ? 'X-RAY DIFFRACTION' ? p_plane_restr 0.014 0.020 ? ? 'X-RAY DIFFRACTION' ? p_chiral_restr 0.180 0.150 ? ? 'X-RAY DIFFRACTION' ? p_singtor_nbd 0.204 0.500 ? ? 'X-RAY DIFFRACTION' ? p_multtor_nbd 0.274 0.500 ? ? 'X-RAY DIFFRACTION' ? p_xhyhbond_nbd 0.181 0.500 ? ? 'X-RAY DIFFRACTION' ? p_xyhbond_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? p_planar_tor 2.8 3.0 ? ? 'X-RAY DIFFRACTION' ? p_staggered_tor 18.2 15.0 ? ? 'X-RAY DIFFRACTION' ? p_orthonormal_tor 28.8 20.0 ? ? 'X-RAY DIFFRACTION' ? p_transverse_tor ? ? ? ? 'X-RAY DIFFRACTION' ? p_special_tor ? ? ? ? 'X-RAY DIFFRACTION' ? # _struct.entry_id 1DFN _struct.title 'CRYSTAL STRUCTURE OF DEFENSIN HNP-3, AN AMPHIPHILIC DIMER: MECHANISMS OF MEMBRANE PERMEABILIZATION' _struct.pdbx_descriptor 'DEFENSIN HNP-3' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1DFN _struct_keywords.pdbx_keywords DEFENSIN _struct_keywords.text DEFENSIN # 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 1 ? C N N 2 ? D N N 2 ? # _struct_biol.id 1 _struct_biol.details ;THE TWO MOLECULES IN THE ASYMMETRIC UNIT HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *A* AND *B*. EACH OF THE TWO MONOMERS IN THE ASYMMETRIC UNIT CONTAINS A THREE STRAND ANTIPARALLEL SHEET. A LOCAL TWO-FOLD AXIS RELATING MOLECULES *A* AND *B* RESULTS IN A SIX-STRANDED ANTIPARALLEL SHEET IN THE DIMER. THE TWO MOLECULES IN THE ASYMMETRIC UNIT ARE RELATED TO EACH OTHER BY A LOCAL TWO-FOLD AXIS. ; _struct_biol.pdbx_parent_biol_id ? # 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 disulf1 disulf ? ? A CYS 2 SG ? ? ? 1_555 A CYS 30 SG ? ? A CYS 3 A CYS 31 1_555 ? ? ? ? ? ? ? 1.966 ? disulf2 disulf ? ? A CYS 4 SG ? ? ? 1_555 A CYS 19 SG ? ? A CYS 5 A CYS 20 1_555 ? ? ? ? ? ? ? 1.967 ? disulf3 disulf ? ? A CYS 9 SG ? ? ? 1_555 A CYS 29 SG ? ? A CYS 10 A CYS 30 1_555 ? ? ? ? ? ? ? 1.932 ? disulf4 disulf ? ? B CYS 2 SG ? ? ? 1_555 B CYS 30 SG ? ? B CYS 3 B CYS 31 1_555 ? ? ? ? ? ? ? 2.011 ? disulf5 disulf ? ? B CYS 4 SG ? ? ? 1_555 B CYS 19 SG ? ? B CYS 5 B CYS 20 1_555 ? ? ? ? ? ? ? 1.979 ? disulf6 disulf ? ? B CYS 9 SG ? ? ? 1_555 B CYS 29 SG ? ? B CYS 10 B CYS 30 1_555 ? ? ? ? ? ? ? 1.961 ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 ILE 6 A . ? ILE 7 A PRO 7 A ? PRO 8 A 1 2.87 2 ILE 6 B . ? ILE 7 B PRO 7 B ? PRO 8 B 1 -0.02 # _struct_sheet.id SAB _struct_sheet.type ? _struct_sheet.number_strands 6 _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 SAB 1 2 ? anti-parallel SAB 2 3 ? anti-parallel SAB 3 4 ? anti-parallel SAB 4 5 ? anti-parallel SAB 5 6 ? 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 SAB 1 TYR A 3 ? ARG A 5 ? TYR A 4 ARG A 6 SAB 2 ARG A 24 ? CYS A 30 ? ARG A 25 CYS A 31 SAB 3 ARG A 14 ? TYR A 21 ? ARG A 15 TYR A 22 SAB 4 ARG B 14 ? TYR B 21 ? ARG B 15 TYR B 22 SAB 5 ARG B 24 ? CYS B 30 ? ARG B 25 CYS B 31 SAB 6 TYR B 3 ? ARG B 5 ? TYR B 4 ARG B 6 # _database_PDB_matrix.entry_id 1DFN _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 1DFN _atom_sites.fract_transf_matrix[1][1] 0.032467 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.022222 _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] 0.024814 _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_sites_footnote.id _atom_sites_footnote.text 1 'RESIDUES A 8 AND B 8 ARE CIS PROLINES.' 2 'THERE IS A CLASSIC BULGE INVOLVING RESIDUES 17, 18, AND 29 FOR EACH OF THE CHAINS.' # loop_ _atom_type.symbol C 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 ASP 1 2 2 ASP ASP A . n A 1 2 CYS 2 3 3 CYS CYS A . n A 1 3 TYR 3 4 4 TYR TYR A . n A 1 4 CYS 4 5 5 CYS CYS A . n A 1 5 ARG 5 6 6 ARG ARG A . n A 1 6 ILE 6 7 7 ILE ILE A . n A 1 7 PRO 7 8 8 PRO PRO A . n A 1 8 ALA 8 9 9 ALA ALA A . n A 1 9 CYS 9 10 10 CYS CYS A . n A 1 10 ILE 10 11 11 ILE ILE A . n A 1 11 ALA 11 12 12 ALA ALA A . n A 1 12 GLY 12 13 13 GLY GLY A . n A 1 13 GLU 13 14 14 GLU GLU A . n A 1 14 ARG 14 15 15 ARG ARG A . n A 1 15 ARG 15 16 16 ARG ARG A . n A 1 16 TYR 16 17 17 TYR TYR A . n A 1 17 GLY 17 18 18 GLY GLY A . n A 1 18 THR 18 19 19 THR THR A . n A 1 19 CYS 19 20 20 CYS CYS A . n A 1 20 ILE 20 21 21 ILE ILE A . n A 1 21 TYR 21 22 22 TYR TYR A . n A 1 22 GLN 22 23 23 GLN GLN A . n A 1 23 GLY 23 24 24 GLY GLY A . n A 1 24 ARG 24 25 25 ARG ARG A . n A 1 25 LEU 25 26 26 LEU LEU A . n A 1 26 TRP 26 27 27 TRP TRP A . n A 1 27 ALA 27 28 28 ALA ALA A . n A 1 28 PHE 28 29 29 PHE PHE A . n A 1 29 CYS 29 30 30 CYS CYS A . n A 1 30 CYS 30 31 31 CYS CYS A . n B 1 1 ASP 1 2 2 ASP ASP B . n B 1 2 CYS 2 3 3 CYS CYS B . n B 1 3 TYR 3 4 4 TYR TYR B . n B 1 4 CYS 4 5 5 CYS CYS B . n B 1 5 ARG 5 6 6 ARG ARG B . n B 1 6 ILE 6 7 7 ILE ILE B . n B 1 7 PRO 7 8 8 PRO PRO B . n B 1 8 ALA 8 9 9 ALA ALA B . n B 1 9 CYS 9 10 10 CYS CYS B . n B 1 10 ILE 10 11 11 ILE ILE B . n B 1 11 ALA 11 12 12 ALA ALA B . n B 1 12 GLY 12 13 13 GLY GLY B . n B 1 13 GLU 13 14 14 GLU GLU B . n B 1 14 ARG 14 15 15 ARG ARG B . n B 1 15 ARG 15 16 16 ARG ARG B . n B 1 16 TYR 16 17 17 TYR TYR B . n B 1 17 GLY 17 18 18 GLY GLY B . n B 1 18 THR 18 19 19 THR THR B . n B 1 19 CYS 19 20 20 CYS CYS B . n B 1 20 ILE 20 21 21 ILE ILE B . n B 1 21 TYR 21 22 22 TYR TYR B . n B 1 22 GLN 22 23 23 GLN GLN B . n B 1 23 GLY 23 24 24 GLY GLY B . n B 1 24 ARG 24 25 25 ARG ARG B . n B 1 25 LEU 25 26 26 LEU LEU B . n B 1 26 TRP 26 27 27 TRP TRP B . n B 1 27 ALA 27 28 28 ALA ALA B . n B 1 28 PHE 28 29 29 PHE PHE B . n B 1 29 CYS 29 30 30 CYS CYS B . n B 1 30 CYS 30 31 31 CYS CYS B . 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 2 HOH 1 32 1 HOH HOH A . C 2 HOH 2 33 2 HOH HOH A . C 2 HOH 3 34 3 HOH HOH A . C 2 HOH 4 35 6 HOH HOH A . C 2 HOH 5 36 9 HOH HOH A . C 2 HOH 6 37 12 HOH HOH A . C 2 HOH 7 38 13 HOH HOH A . C 2 HOH 8 39 14 HOH HOH A . C 2 HOH 9 40 15 HOH HOH A . C 2 HOH 10 41 16 HOH HOH A . C 2 HOH 11 42 18 HOH HOH A . C 2 HOH 12 43 19 HOH HOH A . C 2 HOH 13 44 20 HOH HOH A . C 2 HOH 14 45 21 HOH HOH A . C 2 HOH 15 46 22 HOH HOH A . C 2 HOH 16 47 23 HOH HOH A . C 2 HOH 17 48 25 HOH HOH A . C 2 HOH 18 49 26 HOH HOH A . C 2 HOH 19 50 28 HOH HOH A . C 2 HOH 20 51 29 HOH HOH A . C 2 HOH 21 52 30 HOH HOH A . C 2 HOH 22 53 31 HOH HOH A . C 2 HOH 23 54 32 HOH HOH A . C 2 HOH 24 55 33 HOH HOH A . C 2 HOH 25 56 34 HOH HOH A . C 2 HOH 26 57 35 HOH HOH A . C 2 HOH 27 58 36 HOH HOH A . C 2 HOH 28 59 37 HOH HOH A . C 2 HOH 29 60 38 HOH HOH A . C 2 HOH 30 61 39 HOH HOH A . C 2 HOH 31 62 40 HOH HOH A . C 2 HOH 32 63 43 HOH HOH A . C 2 HOH 33 64 44 HOH HOH A . D 2 HOH 1 32 4 HOH HOH B . D 2 HOH 2 33 5 HOH HOH B . D 2 HOH 3 34 7 HOH HOH B . D 2 HOH 4 35 8 HOH HOH B . D 2 HOH 5 36 10 HOH HOH B . D 2 HOH 6 37 11 HOH HOH B . D 2 HOH 7 38 17 HOH HOH B . D 2 HOH 8 39 24 HOH HOH B . D 2 HOH 9 40 27 HOH HOH B . D 2 HOH 10 41 41 HOH HOH B . D 2 HOH 11 42 42 HOH HOH B . # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA dimeric 2 2 software_defined_assembly PISA tetrameric 4 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,C,D 2 1,2 A,B,C,D # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 850 ? 1 MORE -9 ? 1 'SSA (A^2)' 4160 ? 2 'ABSA (A^2)' 2400 ? 2 MORE -28 ? 2 'SSA (A^2)' 7610 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_665 -x+1,-y+1,z -1.0000000000 0.0000000000 0.0000000000 30.8000000000 0.0000000000 -1.0000000000 0.0000000000 45.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id B _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 35 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id D _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 1992-07-15 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-11-29 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # 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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Derived calculations' 4 4 'Structure model' Other # 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 4 'Structure model' pdbx_database_status 2 4 'Structure model' struct_conf # _pdbx_audit_revision_item.ordinal 1 _pdbx_audit_revision_item.revision_ordinal 4 _pdbx_audit_revision_item.data_content_type 'Structure model' _pdbx_audit_revision_item.item '_pdbx_database_status.process_site' # _software.name PROLSQ _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _pdbx_database_remark.id 700 _pdbx_database_remark.text ;SHEET THERE IS A CLASSIC BULGE INVOLVING RESIDUES 17, 18, AND 29 FOR EACH OF THE CHAINS. ; # _pdbx_entry_details.entry_id 1DFN _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE 30 RESIDUES IN HNP-3 HAVE BEEN NUMBERED FROM 2 - 31 IN ORDER TO BETTER FIT THE SEQUENCE ALIGNMENT WITH OTHER DEFENSIN MOLECULES. ; # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 58 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 59 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.07 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 CA _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 CYS _pdbx_validate_rmsd_bond.auth_seq_id_1 20 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 CB _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 CYS _pdbx_validate_rmsd_bond.auth_seq_id_2 20 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.442 _pdbx_validate_rmsd_bond.bond_target_value 1.526 _pdbx_validate_rmsd_bond.bond_deviation -0.084 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.013 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 CB A TYR 4 ? ? CG A TYR 4 ? ? CD2 A TYR 4 ? ? 115.62 121.00 -5.38 0.60 N 2 1 NE A ARG 16 ? ? CZ A ARG 16 ? ? NH2 A ARG 16 ? ? 123.45 120.30 3.15 0.50 N 3 1 CD A ARG 25 ? ? NE A ARG 25 ? ? CZ A ARG 25 ? ? 114.53 123.60 -9.07 1.40 N 4 1 NH1 A ARG 25 ? ? CZ A ARG 25 ? ? NH2 A ARG 25 ? ? 126.09 119.40 6.69 1.10 N 5 1 NE A ARG 25 ? ? CZ A ARG 25 ? ? NH1 A ARG 25 ? ? 116.30 120.30 -4.00 0.50 N 6 1 NE A ARG 25 ? ? CZ A ARG 25 ? ? NH2 A ARG 25 ? ? 116.78 120.30 -3.52 0.50 N 7 1 NH1 B ARG 6 ? ? CZ B ARG 6 ? ? NH2 B ARG 6 ? ? 112.79 119.40 -6.61 1.10 N 8 1 NE B ARG 6 ? ? CZ B ARG 6 ? ? NH2 B ARG 6 ? ? 125.15 120.30 4.85 0.50 N 9 1 CB B ILE 7 ? ? CA B ILE 7 ? ? C B ILE 7 ? ? 124.76 111.60 13.16 2.00 N 10 1 CA B ILE 11 ? ? CB B ILE 11 ? ? CG2 B ILE 11 ? ? 124.21 110.90 13.31 2.00 N 11 1 CA B ARG 15 ? ? CB B ARG 15 ? ? CG B ARG 15 ? ? 127.60 113.40 14.20 2.20 N 12 1 CD B ARG 16 ? ? NE B ARG 16 ? ? CZ B ARG 16 ? ? 133.06 123.60 9.46 1.40 N 13 1 NE B ARG 16 ? ? CZ B ARG 16 ? ? NH2 B ARG 16 ? ? 124.56 120.30 4.26 0.50 N 14 1 NH1 B ARG 25 ? ? CZ B ARG 25 ? ? NH2 B ARG 25 ? ? 111.52 119.40 -7.88 1.10 N 15 1 NE B ARG 25 ? ? CZ B ARG 25 ? ? NH1 B ARG 25 ? ? 127.52 120.30 7.22 0.50 N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id ARG _pdbx_validate_planes.auth_asym_id A _pdbx_validate_planes.auth_seq_id 25 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.104 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A ARG 15 ? CG ? A ARG 14 CG 2 1 Y 1 A ARG 15 ? CD ? A ARG 14 CD 3 1 Y 1 A ARG 15 ? NE ? A ARG 14 NE 4 1 Y 1 A ARG 15 ? CZ ? A ARG 14 CZ 5 1 Y 1 A ARG 15 ? NH1 ? A ARG 14 NH1 6 1 Y 1 A ARG 15 ? NH2 ? A ARG 14 NH2 7 1 Y 1 B ASP 2 ? OD1 ? B ASP 1 OD1 8 1 Y 1 B ASP 2 ? OD2 ? B ASP 1 OD2 9 1 Y 1 B ARG 15 ? NE ? B ARG 14 NE 10 1 Y 1 B ARG 15 ? CZ ? B ARG 14 CZ 11 1 Y 1 B ARG 15 ? NH1 ? B ARG 14 NH1 12 1 Y 1 B ARG 15 ? NH2 ? B ARG 14 NH2 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #