data_2NXM # _entry.id 2NXM # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.350 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 2NXM pdb_00002nxm 10.2210/pdb2nxm/pdb RCSB RCSB040428 ? ? WWPDB D_1000040428 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1KJG 'Structure of D25N protease bound to the RT-RH substrate peptide' unspecified PDB 2NXD . unspecified PDB 2NXL . unspecified # _pdbx_database_status.entry_id 2NXM _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.recvd_initial_deposition_date 2006-11-17 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry N _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Prabu-Jeyabalan, M.' 1 'Nalivaika, E.' 2 'Schiffer, C.A.' 3 # _citation.id primary _citation.title 'Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease' _citation.journal_abbrev Proteins _citation.journal_volume 70 _citation.page_first 678 _citation.page_last 694 _citation.year 2007 _citation.journal_id_ASTM PSFGEY _citation.country US _citation.journal_id_ISSN 0887-3585 _citation.journal_id_CSD 0867 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17729291 _citation.pdbx_database_id_DOI 10.1002/prot.21514 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Altman, M.D.' 1 ? primary 'Nalivaika, E.A.' 2 ? primary 'Prabu-Jeyabalan, M.' 3 ? primary 'Schiffer, C.A.' 4 ? primary 'Tidor, B.' 5 ? # _cell.entry_id 2NXM _cell.length_a 51.074 _cell.length_b 58.535 _cell.length_c 61.711 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 2NXM _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 19 _symmetry.cell_setting ? _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 'PROTEASE RETROPEPSIN' 10814.805 2 3.4.23.16 'Q7K, D25N, L63P' ? ? 2 polymer syn 'Analogue of RT-RH pol protease substrate peptide' 1028.073 1 ? EP3Q 'decapeptide fragment' ? 3 water nat water 18.015 71 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'HIV-1 PROTEASE' # _entity_name_sys.entity_id 1 _entity_name_sys.name E.C.3.4.23.16 # 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(L)' no no ;PQITLWKRPLVTIRIGGQLKEALLNTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF ; ;PQITLWKRPLVTIRIGGQLKEALLNTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF ; A,B ? 2 'polypeptide(L)' no no GAQTFYVDGA GAQTFYVDGA P ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 PRO n 1 2 GLN n 1 3 ILE n 1 4 THR n 1 5 LEU n 1 6 TRP n 1 7 LYS n 1 8 ARG n 1 9 PRO n 1 10 LEU n 1 11 VAL n 1 12 THR n 1 13 ILE n 1 14 ARG n 1 15 ILE n 1 16 GLY n 1 17 GLY n 1 18 GLN n 1 19 LEU n 1 20 LYS n 1 21 GLU n 1 22 ALA n 1 23 LEU n 1 24 LEU n 1 25 ASN n 1 26 THR n 1 27 GLY n 1 28 ALA n 1 29 ASP n 1 30 ASP n 1 31 THR n 1 32 VAL n 1 33 LEU n 1 34 GLU n 1 35 GLU n 1 36 MET n 1 37 ASN n 1 38 LEU n 1 39 PRO n 1 40 GLY n 1 41 LYS n 1 42 TRP n 1 43 LYS n 1 44 PRO n 1 45 LYS n 1 46 MET n 1 47 ILE n 1 48 GLY n 1 49 GLY n 1 50 ILE n 1 51 GLY n 1 52 GLY n 1 53 PHE n 1 54 ILE n 1 55 LYS n 1 56 VAL n 1 57 ARG n 1 58 GLN n 1 59 TYR n 1 60 ASP n 1 61 GLN n 1 62 ILE n 1 63 PRO n 1 64 ILE n 1 65 GLU n 1 66 ILE n 1 67 CYS n 1 68 GLY n 1 69 HIS n 1 70 LYS n 1 71 ALA n 1 72 ILE n 1 73 GLY n 1 74 THR n 1 75 VAL n 1 76 LEU n 1 77 VAL n 1 78 GLY n 1 79 PRO n 1 80 THR n 1 81 PRO n 1 82 VAL n 1 83 ASN n 1 84 ILE n 1 85 ILE n 1 86 GLY n 1 87 ARG n 1 88 ASN n 1 89 LEU n 1 90 LEU n 1 91 THR n 1 92 GLN n 1 93 ILE n 1 94 GLY n 1 95 CYS n 1 96 THR n 1 97 LEU n 1 98 ASN n 1 99 PHE n 2 1 GLY n 2 2 ALA n 2 3 GLN n 2 4 THR n 2 5 PHE n 2 6 TYR n 2 7 VAL n 2 8 ASP n 2 9 GLY n 2 10 ALA 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 ? _entity_src_gen.gene_src_genus Lentivirus _entity_src_gen.pdbx_gene_src_gene pol _entity_src_gen.gene_src_species 'Human immunodeficiency virus 1' _entity_src_gen.gene_src_strain SF2 _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 'HIV-1 M:B_ARV2/SF2' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 11685 _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 Escherichia _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 Tap106 _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 plasmid _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pXC35 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _pdbx_entity_src_syn.entity_id 2 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'This sequence was custom-designed and then purchased commercially' # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 1 UNP O38732_9HIV1 O38732 1 ;PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF ; ? 2 2 PDB 2NXM 2NXM ? ? ? # 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 2NXM A 1 ? 99 ? O38732 1 ? 99 ? 1 99 2 1 2NXM B 1 ? 99 ? O38732 1 ? 99 ? 1 99 3 2 2NXM P 1 ? 10 ? 2NXM 1 ? 10 ? 1 10 # 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 2NXM LYS A 7 ? UNP O38732 GLN 7 'engineered mutation' 7 1 1 2NXM ASN A 25 ? UNP O38732 ASP 25 'engineered mutation' 25 2 2 2NXM LYS B 7 ? UNP O38732 GLN 7 'engineered mutation' 7 3 2 2NXM ASN B 25 ? UNP O38732 ASP 25 'engineered mutation' 25 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 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 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 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 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 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 2NXM _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.03 _exptl_crystal.density_percent_sol 39.54 _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 298 _exptl_crystal_grow.pH 6.2 _exptl_crystal_grow.pdbx_details '126mM sodium phosphate pH 6.2; 63mM sodium citrate; 25-35% Ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K' _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 200 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2005-03-31 _diffrn_detector.details Yale # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator Yale _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type RIGAKU _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 2NXM _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.d_resolution_high 2.25 _reflns.d_resolution_low 42.49 _reflns.number_all 8523 _reflns.number_obs 8523 _reflns.percent_possible_obs 91.0 _reflns.pdbx_Rmerge_I_obs 0.065 _reflns.pdbx_Rsym_value 0.065 _reflns.pdbx_netI_over_sigmaI 10.3 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.5 _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 ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 2NXM _refine.ls_number_reflns_obs 8037 _refine.ls_number_reflns_all 8037 _refine.pdbx_ls_sigma_I 0 _refine.pdbx_ls_sigma_F 0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 42.49 _refine.ls_d_res_high 2.25 _refine.ls_percent_reflns_obs 91.66 _refine.ls_R_factor_obs 0.18977 _refine.ls_R_factor_all 0.18977 _refine.ls_R_factor_R_work 0.18702 _refine.ls_R_factor_R_free 0.24386 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.8 _refine.ls_number_reflns_R_free 405 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.958 _refine.correlation_coeff_Fo_to_Fc_free 0.922 _refine.B_iso_mean 59.773 _refine.aniso_B[1][1] -2.47 _refine.aniso_B[2][2] 1.91 _refine.aniso_B[3][3] 0.56 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model '1T3R - Crystal Structure of HIV-1 protease bound with TMC114' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model Isotropic _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.444 _refine.pdbx_overall_ESU_R_Free 0.257 _refine.overall_SU_ML 0.186 _refine.overall_SU_B 11.860 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _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.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 1542 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 71 _refine_hist.number_atoms_total 1613 _refine_hist.d_res_high 2.25 _refine_hist.d_res_low 42.49 # 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 r_bond_refined_d 0.008 0.022 ? 1571 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.264 1.974 ? 2142 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 7.224 5.000 ? 203 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 39.553 24.828 ? 58 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 15.778 15.000 ? 253 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 9.234 15.000 ? 8 'X-RAY DIFFRACTION' ? r_chiral_restr 0.088 0.200 ? 256 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.006 0.020 ? 1163 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.214 0.200 ? 640 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.314 0.200 ? 1071 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.157 0.200 ? 85 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.171 0.200 ? 38 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.202 0.200 ? 4 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 0.946 1.500 ? 1040 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1.378 2.000 ? 1640 'X-RAY DIFFRACTION' ? r_scbond_it 2.147 3.000 ? 597 'X-RAY DIFFRACTION' ? r_scangle_it 3.141 4.500 ? 502 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.250 _refine_ls_shell.d_res_low 2.308 _refine_ls_shell.number_reflns_R_work 389 _refine_ls_shell.R_factor_R_work 0.289 _refine_ls_shell.percent_reflns_obs 61.50 _refine_ls_shell.R_factor_R_free 0.269 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 20 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2NXM _struct.title 'Structure of HIV-1 protease D25N complexed with the rt-rh analogue peptide GLY-ALA-GLN-THR-PHE*TYR-VAL-ASP-GLY-ALA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2NXM _struct_keywords.pdbx_keywords 'HYDROLASE/HYDROLASE SUBSTRATE' _struct_keywords.text 'peptide design; molecular dynamics; hiv protease; substrate recognition; calorimetry, HYDROLASE-HYDROLASE SUBSTRATE 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 1 ? C N N 2 ? D N N 3 ? E N N 3 ? F N N 3 ? # 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 GLY A 86 ? THR A 91 ? GLY A 86 THR A 91 1 ? 6 HELX_P HELX_P2 2 GLY B 86 ? THR B 91 ? GLY B 86 THR B 91 1 ? 6 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 9 ? C ? 8 ? # 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 ? anti-parallel A 3 4 ? anti-parallel B 1 2 ? parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel B 4 5 ? parallel B 5 6 ? anti-parallel B 6 7 ? parallel B 7 8 ? anti-parallel B 8 9 ? anti-parallel C 1 2 ? anti-parallel C 2 3 ? anti-parallel C 3 4 ? parallel C 4 5 ? anti-parallel C 5 6 ? parallel C 6 7 ? anti-parallel C 7 8 ? 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 GLN A 2 ? ILE A 3 ? GLN A 2 ILE A 3 A 2 THR B 96 ? ASN B 98 ? THR B 96 ASN B 98 A 3 THR A 96 ? ASN A 98 ? THR A 96 ASN A 98 A 4 GLN B 2 ? THR B 4 ? GLN B 2 THR B 4 B 1 GLN C 3 ? THR C 4 ? GLN P 3 THR P 4 B 2 LYS A 43 ? GLY A 49 ? LYS A 43 GLY A 49 B 3 GLY A 52 ? ILE A 66 ? GLY A 52 ILE A 66 B 4 HIS A 69 ? VAL A 77 ? HIS A 69 VAL A 77 B 5 VAL A 32 ? LEU A 33 ? VAL A 32 LEU A 33 B 6 ILE A 84 ? ILE A 85 ? ILE A 84 ILE A 85 B 7 GLN A 18 ? LEU A 24 ? GLN A 18 LEU A 24 B 8 LEU A 10 ? ILE A 15 ? LEU A 10 ILE A 15 B 9 GLY A 52 ? ILE A 66 ? GLY A 52 ILE A 66 C 1 LYS B 43 ? GLY B 49 ? LYS B 43 GLY B 49 C 2 GLY B 52 ? ILE B 66 ? GLY B 52 ILE B 66 C 3 HIS B 69 ? VAL B 77 ? HIS B 69 VAL B 77 C 4 VAL B 32 ? LEU B 33 ? VAL B 32 LEU B 33 C 5 ILE B 84 ? ILE B 85 ? ILE B 84 ILE B 85 C 6 GLN B 18 ? LEU B 24 ? GLN B 18 LEU B 24 C 7 LEU B 10 ? ILE B 15 ? LEU B 10 ILE B 15 C 8 GLY B 52 ? ILE B 66 ? GLY B 52 ILE B 66 # 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 N ILE A 3 ? N ILE A 3 O LEU B 97 ? O LEU B 97 A 2 3 O THR B 96 ? O THR B 96 N ASN A 98 ? N ASN A 98 A 3 4 N LEU A 97 ? N LEU A 97 O ILE B 3 ? O ILE B 3 B 1 2 O THR C 4 ? O THR P 4 N GLY A 48 ? N GLY A 48 B 2 3 N LYS A 45 ? N LYS A 45 O VAL A 56 ? O VAL A 56 B 3 4 N TYR A 59 ? N TYR A 59 O VAL A 75 ? O VAL A 75 B 4 5 O LEU A 76 ? O LEU A 76 N LEU A 33 ? N LEU A 33 B 5 6 N VAL A 32 ? N VAL A 32 O ILE A 84 ? O ILE A 84 B 6 7 O ILE A 85 ? O ILE A 85 N LEU A 23 ? N LEU A 23 B 7 8 O LYS A 20 ? O LYS A 20 N ILE A 13 ? N ILE A 13 B 8 9 N ARG A 14 ? N ARG A 14 O GLU A 65 ? O GLU A 65 C 1 2 N LYS B 43 ? N LYS B 43 O GLN B 58 ? O GLN B 58 C 2 3 N ILE B 66 ? N ILE B 66 O HIS B 69 ? O HIS B 69 C 3 4 O LEU B 76 ? O LEU B 76 N LEU B 33 ? N LEU B 33 C 4 5 N VAL B 32 ? N VAL B 32 O ILE B 84 ? O ILE B 84 C 5 6 O ILE B 85 ? O ILE B 85 N LEU B 23 ? N LEU B 23 C 6 7 O LYS B 20 ? O LYS B 20 N ILE B 13 ? N ILE B 13 C 7 8 N ARG B 14 ? N ARG B 14 O GLU B 65 ? O GLU B 65 # _atom_sites.entry_id 2NXM _atom_sites.fract_transf_matrix[1][1] 0.019579 _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] 0.017084 _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] 0.016205 _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 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 PRO 1 1 1 PRO PRO 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 THR 4 4 4 THR THR A . n A 1 5 LEU 5 5 5 LEU LEU A . n A 1 6 TRP 6 6 6 TRP TRP A . n A 1 7 LYS 7 7 7 LYS ALA A . n A 1 8 ARG 8 8 8 ARG ARG A . n A 1 9 PRO 9 9 9 PRO PRO A . n A 1 10 LEU 10 10 10 LEU LEU A . n A 1 11 VAL 11 11 11 VAL VAL 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 ARG 14 14 14 ARG ARG A . n A 1 15 ILE 15 15 15 ILE ILE A . n A 1 16 GLY 16 16 16 GLY GLY A . n A 1 17 GLY 17 17 17 GLY GLY A . n A 1 18 GLN 18 18 18 GLN GLN A . n A 1 19 LEU 19 19 19 LEU LEU A . n A 1 20 LYS 20 20 20 LYS ALA A . n A 1 21 GLU 21 21 21 GLU GLU A . n A 1 22 ALA 22 22 22 ALA ALA A . n A 1 23 LEU 23 23 23 LEU LEU A . n A 1 24 LEU 24 24 24 LEU LEU A . n A 1 25 ASN 25 25 25 ASN ASN A . n A 1 26 THR 26 26 26 THR THR A . n A 1 27 GLY 27 27 27 GLY GLY A . n A 1 28 ALA 28 28 28 ALA ALA A . n A 1 29 ASP 29 29 29 ASP ASP A . n A 1 30 ASP 30 30 30 ASP ASP A . n A 1 31 THR 31 31 31 THR THR A . n A 1 32 VAL 32 32 32 VAL VAL A . n A 1 33 LEU 33 33 33 LEU LEU A . n A 1 34 GLU 34 34 34 GLU GLU A . n A 1 35 GLU 35 35 35 GLU GLU A . n A 1 36 MET 36 36 36 MET MET A . n A 1 37 ASN 37 37 37 ASN ASN A . n A 1 38 LEU 38 38 38 LEU LEU A . n A 1 39 PRO 39 39 39 PRO PRO A . n A 1 40 GLY 40 40 40 GLY GLY A . n A 1 41 LYS 41 41 41 LYS ALA A . n A 1 42 TRP 42 42 42 TRP TRP A . n A 1 43 LYS 43 43 43 LYS ALA A . n A 1 44 PRO 44 44 44 PRO PRO A . n A 1 45 LYS 45 45 45 LYS ALA A . n A 1 46 MET 46 46 46 MET MET A . n A 1 47 ILE 47 47 47 ILE ILE A . n A 1 48 GLY 48 48 48 GLY GLY A . n A 1 49 GLY 49 49 49 GLY GLY A . n A 1 50 ILE 50 50 50 ILE ALA A . n A 1 51 GLY 51 51 51 GLY GLY A . n A 1 52 GLY 52 52 52 GLY GLY A . n A 1 53 PHE 53 53 53 PHE PHE A . n A 1 54 ILE 54 54 54 ILE ILE A . n A 1 55 LYS 55 55 55 LYS LYS A . n A 1 56 VAL 56 56 56 VAL VAL A . n A 1 57 ARG 57 57 57 ARG ARG A . n A 1 58 GLN 58 58 58 GLN GLN A . n A 1 59 TYR 59 59 59 TYR TYR A . n A 1 60 ASP 60 60 60 ASP ASP A . n A 1 61 GLN 61 61 61 GLN GLN A . n A 1 62 ILE 62 62 62 ILE ILE A . n A 1 63 PRO 63 63 63 PRO PRO A . n A 1 64 ILE 64 64 64 ILE ILE A . n A 1 65 GLU 65 65 65 GLU GLU A . n A 1 66 ILE 66 66 66 ILE ILE A . n A 1 67 CYS 67 67 67 CYS CYS A . n A 1 68 GLY 68 68 68 GLY GLY A . n A 1 69 HIS 69 69 69 HIS HIS A . n A 1 70 LYS 70 70 70 LYS ALA A . n A 1 71 ALA 71 71 71 ALA ALA A . n A 1 72 ILE 72 72 72 ILE ILE A . n A 1 73 GLY 73 73 73 GLY GLY A . n A 1 74 THR 74 74 74 THR THR A . n A 1 75 VAL 75 75 75 VAL VAL A . n A 1 76 LEU 76 76 76 LEU LEU A . n A 1 77 VAL 77 77 77 VAL VAL A . n A 1 78 GLY 78 78 78 GLY GLY A . n A 1 79 PRO 79 79 79 PRO PRO A . n A 1 80 THR 80 80 80 THR THR A . n A 1 81 PRO 81 81 81 PRO PRO A . n A 1 82 VAL 82 82 82 VAL VAL A . n A 1 83 ASN 83 83 83 ASN ASN A . n A 1 84 ILE 84 84 84 ILE ILE A . n A 1 85 ILE 85 85 85 ILE ILE A . n A 1 86 GLY 86 86 86 GLY GLY A . n A 1 87 ARG 87 87 87 ARG ARG A . n A 1 88 ASN 88 88 88 ASN ASN A . n A 1 89 LEU 89 89 89 LEU LEU A . n A 1 90 LEU 90 90 90 LEU LEU A . n A 1 91 THR 91 91 91 THR THR A . n A 1 92 GLN 92 92 92 GLN GLN A . n A 1 93 ILE 93 93 93 ILE ILE A . n A 1 94 GLY 94 94 94 GLY GLY A . n A 1 95 CYS 95 95 95 CYS CYS A . n A 1 96 THR 96 96 96 THR THR A . n A 1 97 LEU 97 97 97 LEU LEU A . n A 1 98 ASN 98 98 98 ASN ASN A . n A 1 99 PHE 99 99 99 PHE PHE A . n B 1 1 PRO 1 1 1 PRO PRO B . n B 1 2 GLN 2 2 2 GLN GLN B . n B 1 3 ILE 3 3 3 ILE ILE B . n B 1 4 THR 4 4 4 THR THR B . n B 1 5 LEU 5 5 5 LEU LEU B . n B 1 6 TRP 6 6 6 TRP TRP B . n B 1 7 LYS 7 7 7 LYS ALA B . n B 1 8 ARG 8 8 8 ARG ARG B . n B 1 9 PRO 9 9 9 PRO PRO B . n B 1 10 LEU 10 10 10 LEU LEU B . n B 1 11 VAL 11 11 11 VAL VAL B . n B 1 12 THR 12 12 12 THR THR B . n B 1 13 ILE 13 13 13 ILE ILE B . n B 1 14 ARG 14 14 14 ARG ARG B . n B 1 15 ILE 15 15 15 ILE ILE B . n B 1 16 GLY 16 16 16 GLY GLY B . n B 1 17 GLY 17 17 17 GLY GLY B . n B 1 18 GLN 18 18 18 GLN GLN B . n B 1 19 LEU 19 19 19 LEU LEU B . n B 1 20 LYS 20 20 20 LYS LYS B . n B 1 21 GLU 21 21 21 GLU GLU B . n B 1 22 ALA 22 22 22 ALA ALA B . n B 1 23 LEU 23 23 23 LEU LEU B . n B 1 24 LEU 24 24 24 LEU LEU B . n B 1 25 ASN 25 25 25 ASN ASN B . n B 1 26 THR 26 26 26 THR THR B . n B 1 27 GLY 27 27 27 GLY GLY B . n B 1 28 ALA 28 28 28 ALA ALA B . n B 1 29 ASP 29 29 29 ASP ASP B . n B 1 30 ASP 30 30 30 ASP ASP B . n B 1 31 THR 31 31 31 THR THR B . n B 1 32 VAL 32 32 32 VAL VAL B . n B 1 33 LEU 33 33 33 LEU LEU B . n B 1 34 GLU 34 34 34 GLU GLU B . n B 1 35 GLU 35 35 35 GLU GLU B . n B 1 36 MET 36 36 36 MET MET B . n B 1 37 ASN 37 37 37 ASN ASN B . n B 1 38 LEU 38 38 38 LEU LEU B . n B 1 39 PRO 39 39 39 PRO PRO B . n B 1 40 GLY 40 40 40 GLY GLY B . n B 1 41 LYS 41 41 41 LYS ALA B . n B 1 42 TRP 42 42 42 TRP TRP B . n B 1 43 LYS 43 43 43 LYS LYS B . n B 1 44 PRO 44 44 44 PRO PRO B . n B 1 45 LYS 45 45 45 LYS LYS B . n B 1 46 MET 46 46 46 MET MET B . n B 1 47 ILE 47 47 47 ILE ILE B . n B 1 48 GLY 48 48 48 GLY GLY B . n B 1 49 GLY 49 49 49 GLY GLY B . n B 1 50 ILE 50 50 50 ILE ILE B . n B 1 51 GLY 51 51 51 GLY GLY B . n B 1 52 GLY 52 52 52 GLY GLY B . n B 1 53 PHE 53 53 53 PHE PHE B . n B 1 54 ILE 54 54 54 ILE ILE B . n B 1 55 LYS 55 55 55 LYS ALA B . n B 1 56 VAL 56 56 56 VAL VAL B . n B 1 57 ARG 57 57 57 ARG ARG B . n B 1 58 GLN 58 58 58 GLN GLN B . n B 1 59 TYR 59 59 59 TYR TYR B . n B 1 60 ASP 60 60 60 ASP ASP B . n B 1 61 GLN 61 61 61 GLN GLN B . n B 1 62 ILE 62 62 62 ILE ILE B . n B 1 63 PRO 63 63 63 PRO PRO B . n B 1 64 ILE 64 64 64 ILE ILE B . n B 1 65 GLU 65 65 65 GLU GLU B . n B 1 66 ILE 66 66 66 ILE ILE B . n B 1 67 CYS 67 67 67 CYS CYS B . n B 1 68 GLY 68 68 68 GLY GLY B . n B 1 69 HIS 69 69 69 HIS HIS B . n B 1 70 LYS 70 70 70 LYS LYS B . n B 1 71 ALA 71 71 71 ALA ALA B . n B 1 72 ILE 72 72 72 ILE ILE B . n B 1 73 GLY 73 73 73 GLY GLY B . n B 1 74 THR 74 74 74 THR THR B . n B 1 75 VAL 75 75 75 VAL VAL B . n B 1 76 LEU 76 76 76 LEU LEU B . n B 1 77 VAL 77 77 77 VAL VAL B . n B 1 78 GLY 78 78 78 GLY GLY B . n B 1 79 PRO 79 79 79 PRO PRO B . n B 1 80 THR 80 80 80 THR THR B . n B 1 81 PRO 81 81 81 PRO PRO B . n B 1 82 VAL 82 82 82 VAL VAL B . n B 1 83 ASN 83 83 83 ASN ASN B . n B 1 84 ILE 84 84 84 ILE ILE B . n B 1 85 ILE 85 85 85 ILE ILE B . n B 1 86 GLY 86 86 86 GLY GLY B . n B 1 87 ARG 87 87 87 ARG ARG B . n B 1 88 ASN 88 88 88 ASN ASN B . n B 1 89 LEU 89 89 89 LEU LEU B . n B 1 90 LEU 90 90 90 LEU LEU B . n B 1 91 THR 91 91 91 THR THR B . n B 1 92 GLN 92 92 92 GLN GLN B . n B 1 93 ILE 93 93 93 ILE ILE B . n B 1 94 GLY 94 94 94 GLY GLY B . n B 1 95 CYS 95 95 95 CYS CYS B . n B 1 96 THR 96 96 96 THR THR B . n B 1 97 LEU 97 97 97 LEU LEU B . n B 1 98 ASN 98 98 98 ASN ASN B . n B 1 99 PHE 99 99 99 PHE PHE B . n C 2 1 GLY 1 1 ? ? ? P . n C 2 2 ALA 2 2 2 ALA ALA P . n C 2 3 GLN 3 3 3 GLN GLN P . n C 2 4 THR 4 4 4 THR THR P . n C 2 5 PHE 5 5 5 PHE PHE P . n C 2 6 TYR 6 6 6 TYR TYR P . n C 2 7 VAL 7 7 7 VAL VAL P . n C 2 8 ASP 8 8 8 ASP ASP P . n C 2 9 GLY 9 9 9 GLY GLY P . n C 2 10 ALA 10 10 ? ? ? P . 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 D 3 HOH 1 100 1 HOH HOH A . D 3 HOH 2 101 5 HOH HOH A . D 3 HOH 3 102 8 HOH HOH A . D 3 HOH 4 103 11 HOH HOH A . D 3 HOH 5 104 14 HOH HOH A . D 3 HOH 6 105 15 HOH HOH A . D 3 HOH 7 106 18 HOH HOH A . D 3 HOH 8 107 21 HOH HOH A . D 3 HOH 9 108 22 HOH HOH A . D 3 HOH 10 109 23 HOH HOH A . D 3 HOH 11 110 24 HOH HOH A . D 3 HOH 12 111 26 HOH HOH A . D 3 HOH 13 112 28 HOH HOH A . D 3 HOH 14 113 30 HOH HOH A . D 3 HOH 15 114 35 HOH HOH A . D 3 HOH 16 115 42 HOH HOH A . D 3 HOH 17 116 43 HOH HOH A . D 3 HOH 18 117 46 HOH HOH A . D 3 HOH 19 118 47 HOH HOH A . D 3 HOH 20 119 49 HOH HOH A . D 3 HOH 21 120 50 HOH HOH A . D 3 HOH 22 121 57 HOH HOH A . D 3 HOH 23 122 58 HOH HOH A . D 3 HOH 24 123 63 HOH HOH A . D 3 HOH 25 124 69 HOH HOH A . D 3 HOH 26 125 70 HOH HOH A . D 3 HOH 27 126 72 HOH HOH A . D 3 HOH 28 127 82 HOH HOH A . D 3 HOH 29 128 83 HOH HOH A . D 3 HOH 30 129 84 HOH HOH A . D 3 HOH 31 130 86 HOH HOH A . D 3 HOH 32 131 93 HOH HOH A . D 3 HOH 33 132 94 HOH HOH A . D 3 HOH 34 133 95 HOH HOH A . D 3 HOH 35 134 97 HOH HOH A . E 3 HOH 1 100 3 HOH HOH B . E 3 HOH 2 101 4 HOH HOH B . E 3 HOH 3 102 10 HOH HOH B . E 3 HOH 4 103 20 HOH HOH B . E 3 HOH 5 104 25 HOH HOH B . E 3 HOH 6 105 27 HOH HOH B . E 3 HOH 7 106 29 HOH HOH B . E 3 HOH 8 107 31 HOH HOH B . E 3 HOH 9 108 32 HOH HOH B . E 3 HOH 10 109 34 HOH HOH B . E 3 HOH 11 110 37 HOH HOH B . E 3 HOH 12 111 39 HOH HOH B . E 3 HOH 13 112 40 HOH HOH B . E 3 HOH 14 113 41 HOH HOH B . E 3 HOH 15 114 44 HOH HOH B . E 3 HOH 16 115 48 HOH HOH B . E 3 HOH 17 116 51 HOH HOH B . E 3 HOH 18 117 52 HOH HOH B . E 3 HOH 19 118 53 HOH HOH B . E 3 HOH 20 119 54 HOH HOH B . E 3 HOH 21 120 55 HOH HOH B . E 3 HOH 22 121 56 HOH HOH B . E 3 HOH 23 122 59 HOH HOH B . E 3 HOH 24 123 60 HOH HOH B . E 3 HOH 25 124 61 HOH HOH B . E 3 HOH 26 125 64 HOH HOH B . E 3 HOH 27 126 71 HOH HOH B . E 3 HOH 28 127 73 HOH HOH B . E 3 HOH 29 128 74 HOH HOH B . E 3 HOH 30 129 81 HOH HOH B . E 3 HOH 31 130 85 HOH HOH B . E 3 HOH 32 131 89 HOH HOH B . E 3 HOH 33 132 91 HOH HOH B . E 3 HOH 34 133 92 HOH HOH B . E 3 HOH 35 134 98 HOH HOH B . F 3 HOH 1 90 90 HOH HOH P . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _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 # _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 2007-09-18 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-18 4 'Structure model' 1 3 2021-10-20 # _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 ? _pdbx_audit_revision_details.details ? # 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' 'Refinement description' 3 4 'Structure model' 'Database references' # 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 3 'Structure model' software 2 4 'Structure model' database_2 3 4 'Structure model' struct_ref_seq_dif # 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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_ref_seq_dif.details' # loop_ _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.pdbx_refine_id 1 ? refined 4.8380 8.9278 28.8866 0.0637 -0.0228 -0.0512 0.0397 -0.0224 -0.0081 3.3038 1.1316 2.6312 -1.9254 1.8571 -0.9596 -0.3359 -0.2861 0.1127 0.0557 0.2569 -0.0177 -0.2066 -0.0652 0.0790 'X-RAY DIFFRACTION' 2 ? refined 4.1418 -3.9031 28.3600 0.0418 -0.0423 -0.0289 0.0503 0.0008 -0.0172 10.9108 3.3386 5.7260 -3.3543 -3.3722 -2.2507 -0.2076 -0.7000 -0.5347 0.2937 -0.0066 0.1775 -0.0766 -0.5067 0.2142 'X-RAY DIFFRACTION' 3 ? refined 5.8912 12.7228 16.6592 0.0460 -0.0901 0.0261 -0.0110 -0.0297 -0.0215 7.8682 0.1106 3.0111 0.6728 -1.2446 -0.4927 0.0435 0.0674 0.6545 -0.1818 0.1148 -0.3979 -0.2426 0.2595 -0.1583 'X-RAY DIFFRACTION' 4 ? refined -0.1364 3.1243 16.9839 0.0245 -0.0006 -0.0189 -0.0106 0.0101 -0.0055 4.8481 1.0788 0.1795 0.9583 -0.9295 -0.2177 -0.0089 0.2321 0.0709 0.0191 -0.1058 -0.0300 -0.0133 0.0812 0.1147 'X-RAY DIFFRACTION' 5 ? refined 10.3139 -0.3507 19.8100 -0.0017 -0.0365 -0.0127 -0.0152 -0.0196 -0.0049 4.7477 1.5018 3.3214 -0.0011 -1.1723 -0.2177 -0.1920 0.1299 -0.1992 0.0408 0.2168 0.2580 -0.0022 0.0869 -0.0248 'X-RAY DIFFRACTION' 6 ? refined -0.4580 -1.5980 3.9605 0.0505 -0.0265 -0.0665 0.0045 0.0128 -0.0047 11.0280 3.1524 0.0100 -0.7613 -0.3041 0.0922 0.0558 0.5638 -0.1663 -0.4802 -0.1005 -0.2966 0.0475 0.2052 0.0447 'X-RAY DIFFRACTION' 7 ? refined 10.2720 -10.3847 11.3720 0.0231 -0.0182 -0.0286 0.0040 0.0028 0.0167 5.8681 2.5528 1.0341 -1.9294 -0.7576 1.5893 0.1035 0.0626 0.2399 0.0452 0.0274 -0.2763 -0.1169 -0.1812 -0.1309 'X-RAY DIFFRACTION' 8 ? refined -13.6226 6.5415 10.1803 -0.0662 0.0031 0.1022 0.0062 -0.0073 -0.0228 0.3087 3.6175 9.8382 -1.0568 -1.7428 5.9657 0.4554 0.2121 0.1859 -0.1880 -0.2374 0.0192 0.1800 -0.5123 -0.2179 'X-RAY DIFFRACTION' 9 ? refined -12.1749 5.1515 24.3527 0.0232 -0.0214 0.0321 -0.0348 0.0337 0.0592 12.3534 1.2527 2.3033 -1.6704 1.0023 1.3750 -0.2883 -0.5165 -0.3693 0.3135 -0.0131 0.2562 -0.0344 -0.1012 0.3015 'X-RAY DIFFRACTION' 10 ? refined -10.4904 7.5421 17.9070 0.0601 -0.0507 0.0041 0.0007 0.0272 0.0231 3.3010 0.0332 0.0400 -0.3309 0.3633 -0.0364 0.0212 0.1788 0.0532 0.1378 -0.2025 0.0294 0.0452 -0.2219 0.1813 'X-RAY DIFFRACTION' 11 ? refined 23.6702 -7.7976 21.2449 -0.0608 -0.0232 0.0256 0.0416 -0.0330 -0.0757 4.9752 9.6694 7.3115 4.3940 0.1937 2.1314 0.1617 0.2138 -0.2174 0.5526 0.2288 -0.1192 0.5274 0.3800 -0.3905 'X-RAY DIFFRACTION' 12 ? refined 22.0795 6.0322 24.8866 -0.0305 -0.0402 -0.0539 -0.0252 -0.0263 0.0606 13.2377 21.3076 8.0468 -7.0288 -4.2368 9.6298 -0.4454 0.1662 -0.0415 0.2914 0.3544 0.5620 -0.2479 0.4004 0.0910 'X-RAY DIFFRACTION' 13 ? refined 20.8932 -0.2639 25.0813 -0.0024 -0.0200 0.0231 0.0172 -0.0275 0.0004 0.4373 4.7606 2.7520 0.1186 0.5109 3.1573 -0.0688 -0.0587 -0.0352 0.0978 0.3042 -0.3041 0.1032 0.4443 -0.2354 'X-RAY DIFFRACTION' 14 ? refined -4.3625 -4.1147 14.5064 0.0071 -0.0099 -0.0071 -0.0262 0.0014 -0.0170 4.0152 1.6865 6.4712 -1.6866 -3.3702 -0.4717 -0.0172 0.0556 0.0015 0.0208 0.0009 0.2011 0.4550 0.1480 0.0163 'X-RAY DIFFRACTION' 15 ? refined 15.0713 0.0694 12.3735 0.0308 0.0421 -0.0813 0.0240 0.0216 -0.0032 6.6046 2.0896 6.6975 -2.2282 -2.5080 3.6185 0.1387 0.6211 0.0612 -0.1032 -0.3285 -0.1013 -0.3752 -0.3916 0.1898 'X-RAY DIFFRACTION' 16 ? refined -3.8243 9.9338 19.6344 0.0318 -0.0026 0.0048 0.0003 -0.0008 0.0192 1.1476 0.0961 0.4313 -0.3321 0.7035 -0.2036 -0.0354 -0.1449 0.1786 -0.0520 0.0326 -0.0827 -0.0178 -0.1637 0.0029 'X-RAY DIFFRACTION' 17 ? refined 13.6561 -0.0785 27.2798 -0.0080 0.0061 0.0007 0.0383 -0.0194 -0.0030 1.3526 6.2201 4.0467 -0.4443 2.1080 1.4584 -0.2703 -0.2648 -0.2845 0.0616 0.2304 -0.0928 -0.1996 0.1299 0.0399 'X-RAY DIFFRACTION' # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.selection_details 1 1 A 1 A 1 A 5 A 5 ? 'X-RAY DIFFRACTION' ? 2 1 A 94 A 94 A 99 A 99 ? 'X-RAY DIFFRACTION' ? 3 1 B 1 B 1 B 5 B 5 ? 'X-RAY DIFFRACTION' ? 4 1 B 94 B 94 B 99 B 99 ? 'X-RAY DIFFRACTION' ? 5 2 A 6 A 6 A 10 A 10 ? 'X-RAY DIFFRACTION' ? 6 3 B 6 B 6 B 10 B 10 ? 'X-RAY DIFFRACTION' ? 7 4 A 23 A 23 A 32 A 32 ? 'X-RAY DIFFRACTION' ? 8 5 B 23 B 23 B 32 B 32 ? 'X-RAY DIFFRACTION' ? 9 6 A 44 A 44 A 55 A 55 ? 'X-RAY DIFFRACTION' ? 10 7 B 44 B 44 B 55 B 55 ? 'X-RAY DIFFRACTION' ? 11 8 A 58 A 58 A 62 A 62 ? 'X-RAY DIFFRACTION' ? 12 9 A 63 A 63 A 68 A 68 ? 'X-RAY DIFFRACTION' ? 13 10 A 69 A 69 A 76 A 76 ? 'X-RAY DIFFRACTION' ? 14 11 B 58 B 58 B 62 B 62 ? 'X-RAY DIFFRACTION' ? 15 12 B 63 B 63 B 68 B 68 ? 'X-RAY DIFFRACTION' ? 16 13 B 69 B 69 B 76 B 76 ? 'X-RAY DIFFRACTION' ? 17 14 A 77 A 77 A 85 A 85 ? 'X-RAY DIFFRACTION' ? 18 15 B 77 B 77 B 85 B 85 ? 'X-RAY DIFFRACTION' ? 19 16 A 86 A 86 A 93 A 93 ? 'X-RAY DIFFRACTION' ? 20 17 B 86 B 86 B 93 B 93 ? 'X-RAY DIFFRACTION' ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal AMoRE phasing . ? 1 REFMAC refinement 5.2 ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 # 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 PRO A 9 ? ? -69.72 75.49 2 1 GLU A 34 ? ? -44.02 159.39 3 1 ASN B 37 ? ? -92.21 59.44 4 1 PHE P 5 ? ? -101.67 47.61 # 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 LYS 7 ? CG ? A LYS 7 CG 2 1 Y 1 A LYS 7 ? CD ? A LYS 7 CD 3 1 Y 1 A LYS 7 ? CE ? A LYS 7 CE 4 1 Y 1 A LYS 7 ? NZ ? A LYS 7 NZ 5 1 Y 1 A LYS 20 ? CG ? A LYS 20 CG 6 1 Y 1 A LYS 20 ? CD ? A LYS 20 CD 7 1 Y 1 A LYS 20 ? CE ? A LYS 20 CE 8 1 Y 1 A LYS 20 ? NZ ? A LYS 20 NZ 9 1 Y 1 A LYS 41 ? CG ? A LYS 41 CG 10 1 Y 1 A LYS 41 ? CD ? A LYS 41 CD 11 1 Y 1 A LYS 41 ? CE ? A LYS 41 CE 12 1 Y 1 A LYS 41 ? NZ ? A LYS 41 NZ 13 1 Y 1 A LYS 43 ? CG ? A LYS 43 CG 14 1 Y 1 A LYS 43 ? CD ? A LYS 43 CD 15 1 Y 1 A LYS 43 ? CE ? A LYS 43 CE 16 1 Y 1 A LYS 43 ? NZ ? A LYS 43 NZ 17 1 Y 1 A LYS 45 ? CG ? A LYS 45 CG 18 1 Y 1 A LYS 45 ? CD ? A LYS 45 CD 19 1 Y 1 A LYS 45 ? CE ? A LYS 45 CE 20 1 Y 1 A LYS 45 ? NZ ? A LYS 45 NZ 21 1 Y 1 A ILE 50 ? CG1 ? A ILE 50 CG1 22 1 Y 1 A ILE 50 ? CG2 ? A ILE 50 CG2 23 1 Y 1 A ILE 50 ? CD1 ? A ILE 50 CD1 24 1 Y 1 A LYS 70 ? CG ? A LYS 70 CG 25 1 Y 1 A LYS 70 ? CD ? A LYS 70 CD 26 1 Y 1 A LYS 70 ? CE ? A LYS 70 CE 27 1 Y 1 A LYS 70 ? NZ ? A LYS 70 NZ 28 1 Y 1 B LYS 7 ? CG ? B LYS 7 CG 29 1 Y 1 B LYS 7 ? CD ? B LYS 7 CD 30 1 Y 1 B LYS 7 ? CE ? B LYS 7 CE 31 1 Y 1 B LYS 7 ? NZ ? B LYS 7 NZ 32 1 Y 1 B LYS 41 ? CG ? B LYS 41 CG 33 1 Y 1 B LYS 41 ? CD ? B LYS 41 CD 34 1 Y 1 B LYS 41 ? CE ? B LYS 41 CE 35 1 Y 1 B LYS 41 ? NZ ? B LYS 41 NZ 36 1 Y 1 B LYS 55 ? CG ? B LYS 55 CG 37 1 Y 1 B LYS 55 ? CD ? B LYS 55 CD 38 1 Y 1 B LYS 55 ? CE ? B LYS 55 CE 39 1 Y 1 B LYS 55 ? NZ ? B LYS 55 NZ # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 P GLY 1 ? C GLY 1 2 1 Y 1 P ALA 10 ? C ALA 10 # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #