data_2VY1 # _entry.id 2VY1 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2VY1 PDBE EBI-36878 WWPDB D_1290036878 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2VY2 _pdbx_database_related.content_type unspecified _pdbx_database_related.details 'STRUCTURE OF LEAFY TRANSCRIPTION FACTOR FROM ARABIDOPSIS THALIANA IN COMPLEX WITH DNA FROM AG-I PROMOTER' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2VY1 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2008-07-16 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hames, C.' 1 'Ptchelkine, D.' 2 'Grimm, C.' 3 'Thevenon, E.' 4 'Moyroud, E.' 5 'Gerard, F.' 6 'Martiel, J.L.' 7 'Benlloch, R.' 8 'Parcy, F.' 9 'Muller, C.W.' 10 # _citation.id primary _citation.title 'Structural Basis for Leafy Floral Switch Function and Similarity with Helix-Turn-Helix Proteins.' _citation.journal_abbrev 'Embo J.' _citation.journal_volume 27 _citation.page_first 2628 _citation.page_last ? _citation.year 2008 _citation.journal_id_ASTM EMJODG _citation.country UK _citation.journal_id_ISSN 0261-4189 _citation.journal_id_CSD 0897 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18784751 _citation.pdbx_database_id_DOI 10.1038/EMBOJ.2008.184 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Hames, C.' 1 primary 'Ptchelkine, D.' 2 primary 'Grimm, C.' 3 primary 'Thevenon, E.' 4 primary 'Moyroud, E.' 5 primary 'Gerard, F.' 6 primary 'Martiel, J.L.' 7 primary 'Benlloch, R.' 8 primary 'Parcy, F.' 9 primary 'Muller, C.W.' 10 # _cell.entry_id 2VY1 _cell.length_a 98.390 _cell.length_b 98.390 _cell.length_c 176.440 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VY1 _symmetry.space_group_name_H-M 'P 65 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 # 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 'PROTEIN LEAFY' 21892.002 1 ? ? 'DNA BINDING DOMAIN, RESIDUES 231-424' NONE 2 polymer syn ;5'-D(*TP*TP*AP*CP*GP*GP*AP*CP*CP*AP *CP*TP*GP*GP*TP*CP*CP*TP*TP*CP)-3' ; 6208.030 1 ? ? ? ? 3 water nat water 18.015 68 ? ? ? ? # loop_ _entity_name_com.entity_id _entity_name_com.name 1 LEAFY 2 'DNA AP1 SITE' # 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 ;LGTERQREHPFIVTEPGEVARGKKNGLDYLFHLYEQCREFLLQVQTIAKDRGEKCPTKVTNQVFRYAKKSGASYINKPKM RHYVHCYALHCLDEEASNALRRAFKERGENVGSWRQACYKPLVNIACRHGWDIDAVFNAHPRLSIWYVPTKLRQLCHLER NNAVAAAAALVGGISCTGSSTSGRGGCGGDDLRF ; ;LGTERQREHPFIVTEPGEVARGKKNGLDYLFHLYEQCREFLLQVQTIAKDRGEKCPTKVTNQVFRYAKKSGASYINKPKM RHYVHCYALHCLDEEASNALRRAFKERGENVGSWRQACYKPLVNIACRHGWDIDAVFNAHPRLSIWYVPTKLRQLCHLER NNAVAAAAALVGGISCTGSSTSGRGGCGGDDLRF ; A ? 2 polydeoxyribonucleotide no no '(DA)(DG)(DA)(DA)(DG)(DG)(DA)(DC)(DC)(DA)(DG)(DT)(DG)(DG)(DT)(DC)(DC)(DG)(DT)(DA)' AGAAGGACCAGTGGTCCGTA W ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 LEU n 1 2 GLY n 1 3 THR n 1 4 GLU n 1 5 ARG n 1 6 GLN n 1 7 ARG n 1 8 GLU n 1 9 HIS n 1 10 PRO n 1 11 PHE n 1 12 ILE n 1 13 VAL n 1 14 THR n 1 15 GLU n 1 16 PRO n 1 17 GLY n 1 18 GLU n 1 19 VAL n 1 20 ALA n 1 21 ARG n 1 22 GLY n 1 23 LYS n 1 24 LYS n 1 25 ASN n 1 26 GLY n 1 27 LEU n 1 28 ASP n 1 29 TYR n 1 30 LEU n 1 31 PHE n 1 32 HIS n 1 33 LEU n 1 34 TYR n 1 35 GLU n 1 36 GLN n 1 37 CYS n 1 38 ARG n 1 39 GLU n 1 40 PHE n 1 41 LEU n 1 42 LEU n 1 43 GLN n 1 44 VAL n 1 45 GLN n 1 46 THR n 1 47 ILE n 1 48 ALA n 1 49 LYS n 1 50 ASP n 1 51 ARG n 1 52 GLY n 1 53 GLU n 1 54 LYS n 1 55 CYS n 1 56 PRO n 1 57 THR n 1 58 LYS n 1 59 VAL n 1 60 THR n 1 61 ASN n 1 62 GLN n 1 63 VAL n 1 64 PHE n 1 65 ARG n 1 66 TYR n 1 67 ALA n 1 68 LYS n 1 69 LYS n 1 70 SER n 1 71 GLY n 1 72 ALA n 1 73 SER n 1 74 TYR n 1 75 ILE n 1 76 ASN n 1 77 LYS n 1 78 PRO n 1 79 LYS n 1 80 MET n 1 81 ARG n 1 82 HIS n 1 83 TYR n 1 84 VAL n 1 85 HIS n 1 86 CYS n 1 87 TYR n 1 88 ALA n 1 89 LEU n 1 90 HIS n 1 91 CYS n 1 92 LEU n 1 93 ASP n 1 94 GLU n 1 95 GLU n 1 96 ALA n 1 97 SER n 1 98 ASN n 1 99 ALA n 1 100 LEU n 1 101 ARG n 1 102 ARG n 1 103 ALA n 1 104 PHE n 1 105 LYS n 1 106 GLU n 1 107 ARG n 1 108 GLY n 1 109 GLU n 1 110 ASN n 1 111 VAL n 1 112 GLY n 1 113 SER n 1 114 TRP n 1 115 ARG n 1 116 GLN n 1 117 ALA n 1 118 CYS n 1 119 TYR n 1 120 LYS n 1 121 PRO n 1 122 LEU n 1 123 VAL n 1 124 ASN n 1 125 ILE n 1 126 ALA n 1 127 CYS n 1 128 ARG n 1 129 HIS n 1 130 GLY n 1 131 TRP n 1 132 ASP n 1 133 ILE n 1 134 ASP n 1 135 ALA n 1 136 VAL n 1 137 PHE n 1 138 ASN n 1 139 ALA n 1 140 HIS n 1 141 PRO n 1 142 ARG n 1 143 LEU n 1 144 SER n 1 145 ILE n 1 146 TRP n 1 147 TYR n 1 148 VAL n 1 149 PRO n 1 150 THR n 1 151 LYS n 1 152 LEU n 1 153 ARG n 1 154 GLN n 1 155 LEU n 1 156 CYS n 1 157 HIS n 1 158 LEU n 1 159 GLU n 1 160 ARG n 1 161 ASN n 1 162 ASN n 1 163 ALA n 1 164 VAL n 1 165 ALA n 1 166 ALA n 1 167 ALA n 1 168 ALA n 1 169 ALA n 1 170 LEU n 1 171 VAL n 1 172 GLY n 1 173 GLY n 1 174 ILE n 1 175 SER n 1 176 CYS n 1 177 THR n 1 178 GLY n 1 179 SER n 1 180 SER n 1 181 THR n 1 182 SER n 1 183 GLY n 1 184 ARG n 1 185 GLY n 1 186 GLY n 1 187 CYS n 1 188 GLY n 1 189 GLY n 1 190 ASP n 1 191 ASP n 1 192 LEU n 1 193 ARG n 1 194 PHE n 2 1 DA y 2 1 DT y 2 2 DG y 2 2 DT y 2 3 DA n 2 4 DA y 2 4 DC y 2 5 DG n 2 6 DG n 2 7 DA n 2 8 DC n 2 9 DC n 2 10 DA n 2 11 DG y 2 11 DC y 2 12 DT n 2 13 DG n 2 14 DG n 2 15 DT n 2 16 DC n 2 17 DC n 2 18 DG y 2 18 DT y 2 19 DT n 2 20 DA y 2 20 DC y # _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 'MOUSE-EAR CRESS' _entity_src_gen.gene_src_genus ? _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 'FLOWER MERISTEM' _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 'ARABIDOPSIS THALIANA' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 3702 _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 FLOWER _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 469008 _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 'BL21(DE3)' _entity_src_gen.pdbx_host_org_variant 'ROSETTABLUE PLYS' _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 PLASMID _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name PETM-11 _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 'ARABIDOPSIS THALIANA' _pdbx_entity_src_syn.organism_common_name 'MOUSE-EAR CRESS' _pdbx_entity_src_syn.ncbi_taxonomy_id 3702 _pdbx_entity_src_syn.details ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 UNP LFY_ARATH 1 ? ? Q00958 ? 2 PDB 2VY1 2 ? ? 2VY1 ? # 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 2VY1 A 1 ? 194 ? Q00958 231 ? 424 ? 231 424 2 2 2VY1 W 1 ? 20 ? 2VY1 1 ? 20 ? 1 20 # 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 2 2VY1 DT W 1 ? PDB 2VY1 DA 1 microheterogeneity 1 1 2 2VY1 DT W 2 ? PDB 2VY1 DG 2 microheterogeneity 2 2 2 2VY1 DC W 4 ? PDB 2VY1 DA 4 microheterogeneity 4 3 2 2VY1 DC W 11 ? PDB 2VY1 DG 11 microheterogeneity 11 4 2 2VY1 DT W 18 ? PDB 2VY1 DG 18 microheterogeneity 18 5 2 2VY1 DC W 20 ? PDB 2VY1 DA 20 microheterogeneity 20 6 # 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 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 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 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 2VY1 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 5.14 _exptl_crystal.density_percent_sol 78.63 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '10% PEG 400, 100 MM KCL, 10 MM CACL2, 50 MM HEPES (NAOH) PH 7.0' # _diffrn.id 1 _diffrn.ambient_temp 77 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2007-06-21 _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 DIAMOND _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.934 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID14-1' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID14-1 _diffrn_source.pdbx_wavelength 0.934 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2VY1 _reflns.observed_criterion_sigma_I 3.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20.00 _reflns.d_resolution_high 2.10 _reflns.number_obs 29859 _reflns.number_all ? _reflns.percent_possible_obs 97.4 _reflns.pdbx_Rmerge_I_obs 0.05 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 38.50 _reflns.B_iso_Wilson_estimate 41.43 _reflns.pdbx_redundancy 16.9 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.10 _reflns_shell.d_res_low 2.20 _reflns_shell.percent_possible_all 83.9 _reflns_shell.Rmerge_I_obs 0.54 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 5.00 _reflns_shell.pdbx_redundancy 12 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2VY1 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 29857 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.38 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 19.429 _refine.ls_d_res_high 2.104 _refine.ls_percent_reflns_obs 99.52 _refine.ls_R_factor_obs 0.2259 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2245 _refine.ls_R_factor_R_free 0.2515 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.09 _refine.ls_number_reflns_R_free 1521 _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 44.76 _refine.aniso_B[1][1] 1.5315 _refine.aniso_B[2][2] 1.5315 _refine.aniso_B[3][3] -3.0631 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.451 _refine.solvent_model_param_bsol 73.693 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model NONE _refine.pdbx_method_to_determine_struct SIRAS _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 0.27 _refine.pdbx_overall_phase_error 21.66 _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_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1326 _refine_hist.pdbx_number_atoms_nucleic_acid 527 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 68 _refine_hist.number_atoms_total 1921 _refine_hist.d_res_high 2.104 _refine_hist.d_res_low 19.429 # 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 ? ? 1983 'X-RAY DIFFRACTION' ? f_angle_d 1.026 ? ? 2803 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 22.301 ? ? 778 'X-RAY DIFFRACTION' ? f_chiral_restr 0.055 ? ? 295 'X-RAY DIFFRACTION' ? f_plane_restr 0.003 ? ? 273 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all 'X-RAY DIFFRACTION' . 2.1037 2.1716 2493 0.2519 98.00 0.2722 . . 122 . . 'X-RAY DIFFRACTION' . 2.1716 2.2491 2535 0.2528 100.00 0.2621 . . 137 . . 'X-RAY DIFFRACTION' . 2.2491 2.3390 2528 0.2397 100.00 0.2645 . . 144 . . 'X-RAY DIFFRACTION' . 2.3390 2.4452 2528 0.2303 100.00 0.2668 . . 143 . . 'X-RAY DIFFRACTION' . 2.4452 2.5739 2533 0.2403 100.00 0.2564 . . 144 . . 'X-RAY DIFFRACTION' . 2.5739 2.7347 2579 0.2320 100.00 0.2633 . . 139 . . 'X-RAY DIFFRACTION' . 2.7347 2.9452 2551 0.2334 100.00 0.2540 . . 137 . . 'X-RAY DIFFRACTION' . 2.9452 3.2404 2598 0.2310 100.00 0.2834 . . 125 . . 'X-RAY DIFFRACTION' . 3.2404 3.7064 2606 0.2078 100.00 0.2248 . . 156 . . 'X-RAY DIFFRACTION' . 3.7064 4.6591 2656 0.1849 100.00 0.2342 . . 138 . . 'X-RAY DIFFRACTION' . 4.6591 19.4300 2729 0.2189 97.00 0.2415 . . 136 . . # _struct.entry_id 2VY1 _struct.title 'Structure of LEAFY transcription factor from Arabidopsis thaliana in complex with DNA from AP1 promoter' _struct.pdbx_descriptor 'PROTEIN LEAFY' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2VY1 _struct_keywords.pdbx_keywords TRANSCRIPTION _struct_keywords.text ;DNA-BINDING, POLYMORPHISM, TRANSCRIPTION, DEVELOPMENTAL PROTEIN, TRANSCRIPTION REGULATION, HOMEOTIC GENES, FLOWERING, NUCLEUS, DIFFERENTIATION, FLOWER DEVELOPMENT, ACTIVATOR, COILED COIL ; # 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 3 ? # _struct_biol.id 1 # 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 26 ? ARG A 51 ? GLY A 256 ARG A 281 1 ? 26 HELX_P HELX_P2 2 THR A 60 ? SER A 70 ? THR A 290 SER A 300 1 ? 11 HELX_P HELX_P3 3 ASN A 76 ? TYR A 83 ? ASN A 306 TYR A 313 1 ? 8 HELX_P HELX_P4 4 TYR A 83 ? ASP A 93 ? TYR A 313 ASP A 323 1 ? 11 HELX_P HELX_P5 5 ASP A 93 ? ARG A 107 ? ASP A 323 ARG A 337 1 ? 15 HELX_P HELX_P6 6 ASN A 110 ? CYS A 118 ? ASN A 340 CYS A 348 1 ? 9 HELX_P HELX_P7 7 CYS A 118 ? ARG A 128 ? CYS A 348 ARG A 358 1 ? 11 HELX_P HELX_P8 8 ASP A 132 ? HIS A 140 ? ASP A 362 HIS A 370 1 ? 9 HELX_P HELX_P9 9 ARG A 142 ? TRP A 146 ? ARG A 372 TRP A 376 5 ? 5 HELX_P HELX_P10 10 PRO A 149 ? ALA A 167 ? PRO A 379 ALA A 397 1 ? 19 # _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 hydrog1 hydrog ? ? B DG 2 O6 A ? ? 1_555 B DA 20 N6 A ? W DG 2 W DA 20 8_555 ? ? ? ? ? ? 'DG-DA MISPAIR' ? ? hydrog2 hydrog ? ? B DA 3 N1 ? ? ? 1_555 B DT 19 N3 ? ? W DA 3 W DT 19 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? B DA 3 N6 ? ? ? 1_555 B DT 19 O4 ? ? W DA 3 W DT 19 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? B DA 4 N1 A ? ? 1_555 B DG 18 N1 A ? W DA 4 W DG 18 8_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? hydrog5 hydrog ? ? B DA 4 N6 A ? ? 1_555 B DG 18 O6 A ? W DA 4 W DG 18 8_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? hydrog6 hydrog ? ? B DG 5 N1 ? ? ? 1_555 B DC 17 N3 ? ? W DG 5 W DC 17 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? B DG 5 N2 ? ? ? 1_555 B DC 17 O2 ? ? W DG 5 W DC 17 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? B DG 5 O6 ? ? ? 1_555 B DC 17 N4 ? ? W DG 5 W DC 17 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? B DG 6 N1 ? ? ? 1_555 B DC 16 N3 ? ? W DG 6 W DC 16 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? B DG 6 N2 ? ? ? 1_555 B DC 16 O2 ? ? W DG 6 W DC 16 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? B DG 6 O6 ? ? ? 1_555 B DC 16 N4 ? ? W DG 6 W DC 16 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? B DA 7 N1 ? ? ? 1_555 B DT 15 N3 ? ? W DA 7 W DT 15 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? B DA 7 N6 ? ? ? 1_555 B DT 15 O4 ? ? W DA 7 W DT 15 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? B DC 8 N3 ? ? ? 1_555 B DG 14 N1 ? ? W DC 8 W DG 14 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? B DC 8 N4 ? ? ? 1_555 B DG 14 O6 ? ? W DC 8 W DG 14 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? B DC 8 O2 ? ? ? 1_555 B DG 14 N2 ? ? W DC 8 W DG 14 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? B DC 9 N3 ? ? ? 1_555 B DG 13 N1 ? ? W DC 9 W DG 13 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? B DC 9 N4 ? ? ? 1_555 B DG 13 O6 ? ? W DC 9 W DG 13 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? B DC 9 O2 ? ? ? 1_555 B DG 13 N2 ? ? W DC 9 W DG 13 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? B DA 10 N1 ? ? ? 1_555 B DT 12 N3 ? ? W DA 10 W DT 12 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? B DA 10 N6 ? ? ? 1_555 B DT 12 O4 ? ? W DA 10 W DT 12 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? B DG 11 N1 A ? ? 1_555 B DG 11 O6 A ? W DG 11 W DG 11 8_555 ? ? ? ? ? ? TYPE_3_PAIR ? ? hydrog23 hydrog ? ? B DG 11 O6 A ? ? 1_555 B DG 11 N1 A ? W DG 11 W DG 11 8_555 ? ? ? ? ? ? TYPE_3_PAIR ? ? hydrog24 hydrog ? ? B DT 12 N3 ? ? ? 1_555 B DA 10 N1 ? ? W DT 12 W DA 10 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog25 hydrog ? ? B DT 12 O4 ? ? ? 1_555 B DA 10 N6 ? ? W DT 12 W DA 10 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog26 hydrog ? ? B DG 13 N1 ? ? ? 1_555 B DC 9 N3 ? ? W DG 13 W DC 9 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog27 hydrog ? ? B DG 13 N2 ? ? ? 1_555 B DC 9 O2 ? ? W DG 13 W DC 9 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog28 hydrog ? ? B DG 13 O6 ? ? ? 1_555 B DC 9 N4 ? ? W DG 13 W DC 9 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog29 hydrog ? ? B DG 14 N1 ? ? ? 1_555 B DC 8 N3 ? ? W DG 14 W DC 8 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog30 hydrog ? ? B DG 14 N2 ? ? ? 1_555 B DC 8 O2 ? ? W DG 14 W DC 8 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog31 hydrog ? ? B DG 14 O6 ? ? ? 1_555 B DC 8 N4 ? ? W DG 14 W DC 8 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog32 hydrog ? ? B DT 15 N3 ? ? ? 1_555 B DA 7 N1 ? ? W DT 15 W DA 7 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog33 hydrog ? ? B DT 15 O4 ? ? ? 1_555 B DA 7 N6 ? ? W DT 15 W DA 7 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog34 hydrog ? ? B DC 16 N3 ? ? ? 1_555 B DG 6 N1 ? ? W DC 16 W DG 6 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog35 hydrog ? ? B DC 16 N4 ? ? ? 1_555 B DG 6 O6 ? ? W DC 16 W DG 6 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog36 hydrog ? ? B DC 16 O2 ? ? ? 1_555 B DG 6 N2 ? ? W DC 16 W DG 6 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog37 hydrog ? ? B DC 17 N3 ? ? ? 1_555 B DG 5 N1 ? ? W DC 17 W DG 5 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog38 hydrog ? ? B DC 17 N4 ? ? ? 1_555 B DG 5 O6 ? ? W DC 17 W DG 5 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog39 hydrog ? ? B DC 17 O2 ? ? ? 1_555 B DG 5 N2 ? ? W DC 17 W DG 5 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog40 hydrog ? ? B DG 18 N1 A ? ? 1_555 B DA 4 N1 A ? W DG 18 W DA 4 8_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? hydrog41 hydrog ? ? B DG 18 O6 A ? ? 1_555 B DA 4 N6 A ? W DG 18 W DA 4 8_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? hydrog42 hydrog ? ? B DT 19 N3 ? ? ? 1_555 B DA 3 N1 ? ? W DT 19 W DA 3 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog43 hydrog ? ? B DT 19 O4 ? ? ? 1_555 B DA 3 N6 ? ? W DT 19 W DA 3 8_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog44 hydrog ? ? B DA 20 N6 A ? ? 1_555 B DG 2 O6 A ? W DA 20 W DG 2 8_555 ? ? ? ? ? ? 'DA-DG MISPAIR' ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 2VY1 _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 2VY1 _atom_sites.fract_transf_matrix[1][1] 0.010164 _atom_sites.fract_transf_matrix[1][2] 0.005868 _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] 0.011736 _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] 0.005668 _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 P 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 LEU 1 231 ? ? ? A . n A 1 2 GLY 2 232 ? ? ? A . n A 1 3 THR 3 233 ? ? ? A . n A 1 4 GLU 4 234 ? ? ? A . n A 1 5 ARG 5 235 ? ? ? A . n A 1 6 GLN 6 236 ? ? ? A . n A 1 7 ARG 7 237 237 ARG ARG A . n A 1 8 GLU 8 238 238 GLU GLU A . n A 1 9 HIS 9 239 239 HIS HIS A . n A 1 10 PRO 10 240 240 PRO PRO A . n A 1 11 PHE 11 241 241 PHE PHE A . n A 1 12 ILE 12 242 242 ILE ILE A . n A 1 13 VAL 13 243 243 VAL VAL A . n A 1 14 THR 14 244 244 THR THR A . n A 1 15 GLU 15 245 245 GLU GLU A . n A 1 16 PRO 16 246 246 PRO PRO A . n A 1 17 GLY 17 247 247 GLY GLY A . n A 1 18 GLU 18 248 248 GLU GLU A . n A 1 19 VAL 19 249 249 VAL VAL A . n A 1 20 ALA 20 250 250 ALA ALA A . n A 1 21 ARG 21 251 251 ARG ARG A . n A 1 22 GLY 22 252 252 GLY GLY A . n A 1 23 LYS 23 253 253 LYS LYS A . n A 1 24 LYS 24 254 254 LYS LYS A . n A 1 25 ASN 25 255 255 ASN ASN A . n A 1 26 GLY 26 256 256 GLY GLY A . n A 1 27 LEU 27 257 257 LEU LEU A . n A 1 28 ASP 28 258 258 ASP ASP A . n A 1 29 TYR 29 259 259 TYR TYR A . n A 1 30 LEU 30 260 260 LEU LEU A . n A 1 31 PHE 31 261 261 PHE PHE A . n A 1 32 HIS 32 262 262 HIS HIS A . n A 1 33 LEU 33 263 263 LEU LEU A . n A 1 34 TYR 34 264 264 TYR TYR A . n A 1 35 GLU 35 265 265 GLU GLU A . n A 1 36 GLN 36 266 266 GLN GLN A . n A 1 37 CYS 37 267 267 CYS CYS A . n A 1 38 ARG 38 268 268 ARG ARG A . n A 1 39 GLU 39 269 269 GLU GLU A . n A 1 40 PHE 40 270 270 PHE PHE A . n A 1 41 LEU 41 271 271 LEU LEU A . n A 1 42 LEU 42 272 272 LEU LEU A . n A 1 43 GLN 43 273 273 GLN GLN A . n A 1 44 VAL 44 274 274 VAL VAL A . n A 1 45 GLN 45 275 275 GLN GLN A . n A 1 46 THR 46 276 276 THR THR A . n A 1 47 ILE 47 277 277 ILE ILE A . n A 1 48 ALA 48 278 278 ALA ALA A . n A 1 49 LYS 49 279 279 LYS LYS A . n A 1 50 ASP 50 280 280 ASP ASP A . n A 1 51 ARG 51 281 281 ARG ARG A . n A 1 52 GLY 52 282 282 GLY GLY A . n A 1 53 GLU 53 283 283 GLU GLU A . n A 1 54 LYS 54 284 284 LYS LYS A . n A 1 55 CYS 55 285 285 CYS CYS A . n A 1 56 PRO 56 286 286 PRO PRO A . n A 1 57 THR 57 287 287 THR THR A . n A 1 58 LYS 58 288 288 LYS LYS A . n A 1 59 VAL 59 289 289 VAL VAL A . n A 1 60 THR 60 290 290 THR THR A . n A 1 61 ASN 61 291 291 ASN ASN A . n A 1 62 GLN 62 292 292 GLN GLN A . n A 1 63 VAL 63 293 293 VAL VAL A . n A 1 64 PHE 64 294 294 PHE PHE A . n A 1 65 ARG 65 295 295 ARG ARG A . n A 1 66 TYR 66 296 296 TYR TYR A . n A 1 67 ALA 67 297 297 ALA ALA A . n A 1 68 LYS 68 298 298 LYS LYS A . n A 1 69 LYS 69 299 299 LYS LYS A . n A 1 70 SER 70 300 300 SER SER A . n A 1 71 GLY 71 301 301 GLY GLY A . n A 1 72 ALA 72 302 302 ALA ALA A . n A 1 73 SER 73 303 303 SER SER A . n A 1 74 TYR 74 304 304 TYR TYR A . n A 1 75 ILE 75 305 305 ILE ILE A . n A 1 76 ASN 76 306 306 ASN ASN A . n A 1 77 LYS 77 307 307 LYS LYS A . n A 1 78 PRO 78 308 308 PRO PRO A . n A 1 79 LYS 79 309 309 LYS LYS A . n A 1 80 MET 80 310 310 MET MET A . n A 1 81 ARG 81 311 311 ARG ARG A . n A 1 82 HIS 82 312 312 HIS HIS A . n A 1 83 TYR 83 313 313 TYR TYR A . n A 1 84 VAL 84 314 314 VAL VAL A . n A 1 85 HIS 85 315 315 HIS HIS A . n A 1 86 CYS 86 316 316 CYS CYS A . n A 1 87 TYR 87 317 317 TYR TYR A . n A 1 88 ALA 88 318 318 ALA ALA A . n A 1 89 LEU 89 319 319 LEU LEU A . n A 1 90 HIS 90 320 320 HIS HIS A . n A 1 91 CYS 91 321 321 CYS CYS A . n A 1 92 LEU 92 322 322 LEU LEU A . n A 1 93 ASP 93 323 323 ASP ASP A . n A 1 94 GLU 94 324 324 GLU GLU A . n A 1 95 GLU 95 325 325 GLU GLU A . n A 1 96 ALA 96 326 326 ALA ALA A . n A 1 97 SER 97 327 327 SER SER A . n A 1 98 ASN 98 328 328 ASN ASN A . n A 1 99 ALA 99 329 329 ALA ALA A . n A 1 100 LEU 100 330 330 LEU LEU A . n A 1 101 ARG 101 331 331 ARG ARG A . n A 1 102 ARG 102 332 332 ARG ARG A . n A 1 103 ALA 103 333 333 ALA ALA A . n A 1 104 PHE 104 334 334 PHE PHE A . n A 1 105 LYS 105 335 335 LYS LYS A . n A 1 106 GLU 106 336 336 GLU GLU A . n A 1 107 ARG 107 337 337 ARG ARG A . n A 1 108 GLY 108 338 338 GLY GLY A . n A 1 109 GLU 109 339 339 GLU GLU A . n A 1 110 ASN 110 340 340 ASN ASN A . n A 1 111 VAL 111 341 341 VAL VAL A . n A 1 112 GLY 112 342 342 GLY GLY A . n A 1 113 SER 113 343 343 SER SER A . n A 1 114 TRP 114 344 344 TRP TRP A . n A 1 115 ARG 115 345 345 ARG ARG A . n A 1 116 GLN 116 346 346 GLN GLN A . n A 1 117 ALA 117 347 347 ALA ALA A . n A 1 118 CYS 118 348 348 CYS CYS A . n A 1 119 TYR 119 349 349 TYR TYR A . n A 1 120 LYS 120 350 350 LYS LYS A . n A 1 121 PRO 121 351 351 PRO PRO A . n A 1 122 LEU 122 352 352 LEU LEU A . n A 1 123 VAL 123 353 353 VAL VAL A . n A 1 124 ASN 124 354 354 ASN ASN A . n A 1 125 ILE 125 355 355 ILE ILE A . n A 1 126 ALA 126 356 356 ALA ALA A . n A 1 127 CYS 127 357 357 CYS CYS A . n A 1 128 ARG 128 358 358 ARG ARG A . n A 1 129 HIS 129 359 359 HIS HIS A . n A 1 130 GLY 130 360 360 GLY GLY A . n A 1 131 TRP 131 361 361 TRP TRP A . n A 1 132 ASP 132 362 362 ASP ASP A . n A 1 133 ILE 133 363 363 ILE ILE A . n A 1 134 ASP 134 364 364 ASP ASP A . n A 1 135 ALA 135 365 365 ALA ALA A . n A 1 136 VAL 136 366 366 VAL VAL A . n A 1 137 PHE 137 367 367 PHE PHE A . n A 1 138 ASN 138 368 368 ASN ASN A . n A 1 139 ALA 139 369 369 ALA ALA A . n A 1 140 HIS 140 370 370 HIS HIS A . n A 1 141 PRO 141 371 371 PRO PRO A . n A 1 142 ARG 142 372 372 ARG ARG A . n A 1 143 LEU 143 373 373 LEU LEU A . n A 1 144 SER 144 374 374 SER SER A . n A 1 145 ILE 145 375 375 ILE ILE A . n A 1 146 TRP 146 376 376 TRP TRP A . n A 1 147 TYR 147 377 377 TYR TYR A . n A 1 148 VAL 148 378 378 VAL VAL A . n A 1 149 PRO 149 379 379 PRO PRO A . n A 1 150 THR 150 380 380 THR THR A . n A 1 151 LYS 151 381 381 LYS LYS A . n A 1 152 LEU 152 382 382 LEU LEU A . n A 1 153 ARG 153 383 383 ARG ARG A . n A 1 154 GLN 154 384 384 GLN GLN A . n A 1 155 LEU 155 385 385 LEU LEU A . n A 1 156 CYS 156 386 386 CYS CYS A . n A 1 157 HIS 157 387 387 HIS HIS A . n A 1 158 LEU 158 388 388 LEU LEU A . n A 1 159 GLU 159 389 389 GLU GLU A . n A 1 160 ARG 160 390 390 ARG ARG A . n A 1 161 ASN 161 391 391 ASN ASN A . n A 1 162 ASN 162 392 392 ASN ASN A . n A 1 163 ALA 163 393 393 ALA ALA A . n A 1 164 VAL 164 394 394 VAL VAL A . n A 1 165 ALA 165 395 395 ALA ALA A . n A 1 166 ALA 166 396 396 ALA ALA A . n A 1 167 ALA 167 397 397 ALA ALA A . n A 1 168 ALA 168 398 398 ALA ALA A . n A 1 169 ALA 169 399 399 ALA ALA A . n A 1 170 LEU 170 400 400 LEU LEU A . n A 1 171 VAL 171 401 ? ? ? A . n A 1 172 GLY 172 402 ? ? ? A . n A 1 173 GLY 173 403 ? ? ? A . n A 1 174 ILE 174 404 ? ? ? A . n A 1 175 SER 175 405 ? ? ? A . n A 1 176 CYS 176 406 ? ? ? A . n A 1 177 THR 177 407 ? ? ? A . n A 1 178 GLY 178 408 ? ? ? A . n A 1 179 SER 179 409 ? ? ? A . n A 1 180 SER 180 410 ? ? ? A . n A 1 181 THR 181 411 ? ? ? A . n A 1 182 SER 182 412 ? ? ? A . n A 1 183 GLY 183 413 ? ? ? A . n A 1 184 ARG 184 414 ? ? ? A . n A 1 185 GLY 185 415 ? ? ? A . n A 1 186 GLY 186 416 ? ? ? A . n A 1 187 CYS 187 417 ? ? ? A . n A 1 188 GLY 188 418 ? ? ? A . n A 1 189 GLY 189 419 ? ? ? A . n A 1 190 ASP 190 420 ? ? ? A . n A 1 191 ASP 191 421 ? ? ? A . n A 1 192 LEU 192 422 ? ? ? A . n A 1 193 ARG 193 423 ? ? ? A . n A 1 194 PHE 194 424 ? ? ? A . n B 2 1 DA 1 1 1 DA DA W . y B 2 1 DT 1 1 1 DT DT W . y B 2 2 DG 2 2 2 DG DG W . y B 2 2 DT 2 2 2 DT DT W . y B 2 3 DA 3 3 3 DA DA W . n B 2 4 DA 4 4 4 DA DA W . y B 2 4 DC 4 4 4 DC DC W . y B 2 5 DG 5 5 5 DG DG W . n B 2 6 DG 6 6 6 DG DG W . n B 2 7 DA 7 7 7 DA DA W . n B 2 8 DC 8 8 8 DC DC W . n B 2 9 DC 9 9 9 DC DC W . n B 2 10 DA 10 10 10 DA DA W . n B 2 11 DG 11 11 11 DG DG W . y B 2 11 DC 11 11 11 DC DC W . y B 2 12 DT 12 12 12 DT DT W . n B 2 13 DG 13 13 13 DG DG W . n B 2 14 DG 14 14 14 DG DG W . n B 2 15 DT 15 15 15 DT DT W . n B 2 16 DC 16 16 16 DC DC W . n B 2 17 DC 17 17 17 DC DC W . n B 2 18 DG 18 18 18 DG DG W . y B 2 18 DT 18 18 18 DT DT W . y B 2 19 DT 19 19 19 DT DT W . n B 2 20 DA 20 20 20 DA DA W . y B 2 20 DC 20 20 20 DC DC W . y # 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 HOH 1 2001 2001 HOH HOH A . C 3 HOH 2 2002 2002 HOH HOH A . C 3 HOH 3 2003 2003 HOH HOH A . C 3 HOH 4 2004 2004 HOH HOH A . C 3 HOH 5 2005 2005 HOH HOH A . C 3 HOH 6 2006 2006 HOH HOH A . C 3 HOH 7 2007 2007 HOH HOH A . C 3 HOH 8 2008 2008 HOH HOH A . C 3 HOH 9 2009 2009 HOH HOH A . C 3 HOH 10 2010 2010 HOH HOH A . C 3 HOH 11 2011 2011 HOH HOH A . C 3 HOH 12 2012 2012 HOH HOH A . C 3 HOH 13 2013 2013 HOH HOH A . C 3 HOH 14 2014 2014 HOH HOH A . C 3 HOH 15 2015 2015 HOH HOH A . C 3 HOH 16 2016 2016 HOH HOH A . C 3 HOH 17 2017 2017 HOH HOH A . C 3 HOH 18 2018 2018 HOH HOH A . C 3 HOH 19 2019 2019 HOH HOH A . C 3 HOH 20 2020 2020 HOH HOH A . C 3 HOH 21 2021 2021 HOH HOH A . C 3 HOH 22 2022 2022 HOH HOH A . C 3 HOH 23 2023 2023 HOH HOH A . C 3 HOH 24 2024 2024 HOH HOH A . C 3 HOH 25 2025 2025 HOH HOH A . C 3 HOH 26 2026 2026 HOH HOH A . C 3 HOH 27 2027 2027 HOH HOH A . C 3 HOH 28 2028 2028 HOH HOH A . C 3 HOH 29 2029 2029 HOH HOH A . C 3 HOH 30 2030 2030 HOH HOH A . C 3 HOH 31 2031 2031 HOH HOH A . C 3 HOH 32 2032 2032 HOH HOH A . C 3 HOH 33 2033 2033 HOH HOH A . C 3 HOH 34 2034 2034 HOH HOH A . C 3 HOH 35 2035 2035 HOH HOH A . C 3 HOH 36 2036 2036 HOH HOH A . C 3 HOH 37 2037 2037 HOH HOH A . C 3 HOH 38 2038 2038 HOH HOH A . C 3 HOH 39 2039 2039 HOH HOH A . C 3 HOH 40 2040 2040 HOH HOH A . C 3 HOH 41 2041 2041 HOH HOH A . C 3 HOH 42 2042 2042 HOH HOH A . C 3 HOH 43 2043 2043 HOH HOH A . C 3 HOH 44 2044 2044 HOH HOH A . C 3 HOH 45 2045 2045 HOH HOH A . C 3 HOH 46 2046 2046 HOH HOH A . C 3 HOH 47 2047 2047 HOH HOH A . C 3 HOH 48 2048 2048 HOH HOH A . C 3 HOH 49 2049 2049 HOH HOH A . C 3 HOH 50 2050 2050 HOH HOH A . C 3 HOH 51 2051 2051 HOH HOH A . C 3 HOH 52 2052 2052 HOH HOH A . C 3 HOH 53 2053 2053 HOH HOH A . C 3 HOH 54 2054 2054 HOH HOH A . C 3 HOH 55 2055 2055 HOH HOH A . C 3 HOH 56 2056 2056 HOH HOH A . C 3 HOH 57 2057 2057 HOH HOH A . C 3 HOH 58 2058 2058 HOH HOH A . C 3 HOH 59 2059 2059 HOH HOH A . C 3 HOH 60 2060 2060 HOH HOH A . D 3 HOH 1 2001 2001 HOH HOH W . D 3 HOH 2 2002 2002 HOH HOH W . D 3 HOH 3 2003 2003 HOH HOH W . D 3 HOH 4 2004 2004 HOH HOH W . D 3 HOH 5 2005 2005 HOH HOH W . D 3 HOH 6 2006 2006 HOH HOH W . D 3 HOH 7 2007 2007 HOH HOH W . D 3 HOH 8 2008 2008 HOH HOH W . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list 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)' 6080 ? 1 MORE -29.0 ? 1 'SSA (A^2)' 22440 ? # 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' 8_555 x-y,-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 # 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 2008-09-23 2 'Structure model' 1 1 2013-08-07 # _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' 'Database references' 2 2 'Structure model' 'Derived calculations' 3 2 'Structure model' 'Non-polymer description' 4 2 'Structure model' Other 5 2 'Structure model' 'Refinement description' 6 2 'Structure model' 'Source and taxonomy' 7 2 'Structure model' 'Structure summary' 8 2 'Structure model' 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal PHENIX refinement '(PHENIX.REFINE)' ? 1 XDS 'data reduction' . ? 2 XDS 'data scaling' . ? 3 SHARP phasing . ? 4 # _pdbx_entry_details.entry_id 2VY1 _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;CHAIN W HAS MICROHETEROGENEITY AT POSITIONS 1(DT/DA), 2(DG/DT), 4(DA/DC), 11(DG/DC), 18(DG/DT) AND 20(DA/DC). ; # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 OH _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 TYR _pdbx_validate_symm_contact.auth_seq_id_1 296 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 OH _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 TYR _pdbx_validate_symm_contact.auth_seq_id_2 296 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 12_554 _pdbx_validate_symm_contact.dist 2.11 # 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 "C3'" W DA 1 ? A "C2'" W DA 1 ? A "C1'" W DA 1 ? A 97.22 102.40 -5.18 0.80 N 2 1 "O4'" W DG 11 ? A "C1'" W DG 11 ? A N9 W DG 11 ? A 112.58 108.30 4.28 0.30 N 3 1 "O4'" W DG 14 ? ? "C1'" W DG 14 ? ? N9 W DG 14 ? ? 110.11 108.30 1.81 0.30 N 4 1 "O4'" W DT 15 ? ? "C1'" W DT 15 ? ? N1 W DT 15 ? ? 111.91 108.30 3.61 0.30 N 5 1 "C3'" W DG 18 ? A "C2'" W DG 18 ? A "C1'" W DG 18 ? A 96.96 102.40 -5.44 0.80 N 6 1 "C3'" W DA 20 ? A "C2'" W DA 20 ? A "C1'" W DA 20 ? A 97.48 102.40 -4.92 0.80 N # 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 ALA A 397 ? ? -96.06 32.41 2 1 ALA A 399 ? ? -80.25 48.49 # 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 ALA 399 ? O ? A ALA 169 O 2 1 Y 1 A LEU 400 ? CA ? A LEU 170 CA 3 1 Y 1 A LEU 400 ? C ? A LEU 170 C 4 1 Y 1 A LEU 400 ? O ? A LEU 170 O 5 1 Y 1 A LEU 400 ? CB ? A LEU 170 CB 6 1 Y 1 A LEU 400 ? CG ? A LEU 170 CG 7 1 Y 1 A LEU 400 ? CD1 ? A LEU 170 CD1 8 1 Y 1 A LEU 400 ? CD2 ? A LEU 170 CD2 # 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 A LEU 231 ? A LEU 1 2 1 Y 1 A GLY 232 ? A GLY 2 3 1 Y 1 A THR 233 ? A THR 3 4 1 Y 1 A GLU 234 ? A GLU 4 5 1 Y 1 A ARG 235 ? A ARG 5 6 1 Y 1 A GLN 236 ? A GLN 6 7 1 Y 1 A VAL 401 ? A VAL 171 8 1 Y 1 A GLY 402 ? A GLY 172 9 1 Y 1 A GLY 403 ? A GLY 173 10 1 Y 1 A ILE 404 ? A ILE 174 11 1 Y 1 A SER 405 ? A SER 175 12 1 Y 1 A CYS 406 ? A CYS 176 13 1 Y 1 A THR 407 ? A THR 177 14 1 Y 1 A GLY 408 ? A GLY 178 15 1 Y 1 A SER 409 ? A SER 179 16 1 Y 1 A SER 410 ? A SER 180 17 1 Y 1 A THR 411 ? A THR 181 18 1 Y 1 A SER 412 ? A SER 182 19 1 Y 1 A GLY 413 ? A GLY 183 20 1 Y 1 A ARG 414 ? A ARG 184 21 1 Y 1 A GLY 415 ? A GLY 185 22 1 Y 1 A GLY 416 ? A GLY 186 23 1 Y 1 A CYS 417 ? A CYS 187 24 1 Y 1 A GLY 418 ? A GLY 188 25 1 Y 1 A GLY 419 ? A GLY 189 26 1 Y 1 A ASP 420 ? A ASP 190 27 1 Y 1 A ASP 421 ? A ASP 191 28 1 Y 1 A LEU 422 ? A LEU 192 29 1 Y 1 A ARG 423 ? A ARG 193 30 1 Y 1 A PHE 424 ? A PHE 194 # _ndb_struct_conf_na.entry_id 2VY1 _ndb_struct_conf_na.feature 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 B DG 2 1_555 B DA 20 8_555 -0.687 0.804 -0.265 -6.305 -5.366 -0.268 1 W_DG2:DA20_W W 2 ? W 20 ? ? 1 1 B DA 3 1_555 B DT 19 8_555 0.308 -0.099 0.237 3.093 -8.996 1.317 2 W_DA3:DT19_W W 3 ? W 19 ? 20 1 1 B DA 4 1_555 B DG 18 8_555 0.165 0.997 0.233 -1.971 -13.462 -5.460 3 W_DA4:DG18_W W 4 ? W 18 ? 8 1 1 B DG 5 1_555 B DC 17 8_555 -0.249 -0.123 0.158 5.067 -6.023 1.706 4 W_DG5:DC17_W W 5 ? W 17 ? 19 1 1 B DG 6 1_555 B DC 16 8_555 0.017 -0.266 0.433 -0.343 -20.737 -4.207 5 W_DG6:DC16_W W 6 ? W 16 ? 19 1 1 B DA 7 1_555 B DT 15 8_555 0.097 -0.253 0.025 2.062 2.773 1.430 6 W_DA7:DT15_W W 7 ? W 15 ? 20 1 1 B DC 8 1_555 B DG 14 8_555 0.470 -0.178 -0.108 10.821 -7.834 0.408 7 W_DC8:DG14_W W 8 ? W 14 ? 19 1 1 B DC 9 1_555 B DG 13 8_555 0.260 -0.156 -0.020 7.369 -8.054 0.975 8 W_DC9:DG13_W W 9 ? W 13 ? 19 1 1 B DA 10 1_555 B DT 12 8_555 0.109 -0.140 0.245 10.260 -17.800 -0.805 9 W_DA10:DT12_W W 10 ? W 12 ? 20 1 1 B DG 11 1_555 B DG 11 8_555 0.000 0.898 -0.109 0.000 -13.185 -12.818 10 W_DG11:DG11_W W 11 ? W 11 ? 3 1 1 B DT 12 1_555 B DA 10 8_555 -0.109 -0.140 0.245 -10.260 -17.800 -0.805 11 W_DT12:DA10_W W 12 ? W 10 ? 20 1 1 B DG 13 1_555 B DC 9 8_555 -0.260 -0.156 -0.020 -7.369 -8.054 0.975 12 W_DG13:DC9_W W 13 ? W 9 ? 19 1 1 B DG 14 1_555 B DC 8 8_555 -0.470 -0.178 -0.108 -10.821 -7.834 0.408 13 W_DG14:DC8_W W 14 ? W 8 ? 19 1 1 B DT 15 1_555 B DA 7 8_555 -0.097 -0.253 0.025 -2.062 2.773 1.430 14 W_DT15:DA7_W W 15 ? W 7 ? 20 1 1 B DC 16 1_555 B DG 6 8_555 -0.017 -0.266 0.433 0.343 -20.737 -4.207 15 W_DC16:DG6_W W 16 ? W 6 ? 19 1 1 B DC 17 1_555 B DG 5 8_555 0.249 -0.123 0.158 -5.067 -6.023 1.706 16 W_DC17:DG5_W W 17 ? W 5 ? 19 1 1 B DG 18 1_555 B DA 4 8_555 -0.165 0.997 0.233 1.971 -13.462 -5.460 17 W_DG18:DA4_W W 18 ? W 4 ? 8 1 1 B DT 19 1_555 B DA 3 8_555 -0.308 -0.099 0.237 -3.093 -8.996 1.317 18 W_DT19:DA3_W W 19 ? W 3 ? 20 1 1 B DA 20 1_555 B DG 2 8_555 0.687 0.804 -0.265 6.305 -5.366 -0.268 19 W_DA20:DG2_W W 20 ? W 2 ? ? 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 B DG 2 1_555 B DA 20 8_555 B DA 3 1_555 B DT 19 8_555 0.212 -0.131 3.134 -3.633 2.014 33.602 -0.534 -0.923 3.082 3.467 6.254 33.851 1 WW_DG2DA3:DT19DA20_WW W 2 ? W 20 ? W 3 ? W 19 ? 1 B DA 3 1_555 B DT 19 8_555 B DA 4 1_555 B DG 18 8_555 -1.002 -0.506 3.486 0.013 -1.131 35.812 -0.649 1.630 3.500 -1.838 -0.021 35.829 2 WW_DA3DA4:DG18DT19_WW W 3 ? W 19 ? W 4 ? W 18 ? 1 B DA 4 1_555 B DG 18 8_555 B DG 5 1_555 B DC 17 8_555 1.006 0.653 3.187 5.794 0.818 34.428 0.965 -0.799 3.321 1.370 -9.703 34.907 3 WW_DA4DG5:DC17DG18_WW W 4 ? W 18 ? W 5 ? W 17 ? 1 B DG 5 1_555 B DC 17 8_555 B DG 6 1_555 B DC 16 8_555 -1.424 1.427 3.568 -4.980 -5.360 41.823 2.566 1.415 3.506 -7.440 6.913 42.430 4 WW_DG5DG6:DC16DC17_WW W 5 ? W 17 ? W 6 ? W 16 ? 1 B DG 6 1_555 B DC 16 8_555 B DA 7 1_555 B DT 15 8_555 1.535 0.508 3.431 2.818 -10.869 37.276 2.147 -1.948 3.266 -16.550 -4.290 38.873 5 WW_DG6DA7:DT15DC16_WW W 6 ? W 16 ? W 7 ? W 15 ? 1 B DA 7 1_555 B DT 15 8_555 B DC 8 1_555 B DG 14 8_555 -0.457 -0.145 3.243 -0.435 2.806 31.087 -0.797 0.767 3.224 5.221 0.810 31.214 6 WW_DA7DC8:DG14DT15_WW W 7 ? W 15 ? W 8 ? W 14 ? 1 B DC 8 1_555 B DG 14 8_555 B DC 9 1_555 B DG 13 8_555 -0.510 -0.313 3.385 1.011 7.087 29.660 -2.038 1.175 3.207 13.597 -1.939 30.493 7 WW_DC8DC9:DG13DG14_WW W 8 ? W 14 ? W 9 ? W 13 ? 1 B DC 9 1_555 B DG 13 8_555 B DA 10 1_555 B DT 12 8_555 -0.166 0.990 3.271 0.368 2.169 37.485 1.252 0.306 3.319 3.371 -0.572 37.547 8 WW_DC9DA10:DT12DG13_WW W 9 ? W 13 ? W 10 ? W 12 ? 1 B DA 10 1_555 B DT 12 8_555 B DG 11 1_555 B DG 11 8_555 0.492 -0.643 3.496 1.756 1.163 36.173 -1.209 -0.528 3.493 1.870 -2.826 36.232 9 WW_DA10DG11:DG11DT12_WW W 10 ? W 12 ? W 11 ? W 11 ? 1 B DG 11 1_555 B DG 11 8_555 B DT 12 1_555 B DA 10 8_555 -0.492 -0.643 3.496 -1.756 1.163 36.173 -1.209 0.528 3.493 1.870 2.826 36.232 10 WW_DG11DT12:DA10DG11_WW W 11 ? W 11 ? W 12 ? W 10 ? 1 B DT 12 1_555 B DA 10 8_555 B DG 13 1_555 B DC 9 8_555 0.166 0.990 3.271 -0.368 2.169 37.485 1.252 -0.306 3.319 3.371 0.572 37.547 11 WW_DT12DG13:DC9DA10_WW W 12 ? W 10 ? W 13 ? W 9 ? 1 B DG 13 1_555 B DC 9 8_555 B DG 14 1_555 B DC 8 8_555 0.510 -0.313 3.385 -1.011 7.087 29.660 -2.038 -1.175 3.207 13.597 1.939 30.493 12 WW_DG13DG14:DC8DC9_WW W 13 ? W 9 ? W 14 ? W 8 ? 1 B DG 14 1_555 B DC 8 8_555 B DT 15 1_555 B DA 7 8_555 0.457 -0.145 3.243 0.435 2.806 31.087 -0.797 -0.767 3.224 5.221 -0.810 31.214 13 WW_DG14DT15:DA7DC8_WW W 14 ? W 8 ? W 15 ? W 7 ? 1 B DT 15 1_555 B DA 7 8_555 B DC 16 1_555 B DG 6 8_555 -1.535 0.508 3.431 -2.818 -10.869 37.276 2.147 1.948 3.266 -16.550 4.290 38.873 14 WW_DT15DC16:DG6DA7_WW W 15 ? W 7 ? W 16 ? W 6 ? 1 B DC 16 1_555 B DG 6 8_555 B DC 17 1_555 B DG 5 8_555 1.424 1.427 3.568 4.980 -5.360 41.823 2.566 -1.415 3.506 -7.440 -6.913 42.430 15 WW_DC16DC17:DG5DG6_WW W 16 ? W 6 ? W 17 ? W 5 ? 1 B DC 17 1_555 B DG 5 8_555 B DG 18 1_555 B DA 4 8_555 -1.006 0.653 3.187 -5.794 0.818 34.428 0.965 0.799 3.321 1.370 9.703 34.907 16 WW_DC17DG18:DA4DG5_WW W 17 ? W 5 ? W 18 ? W 4 ? 1 B DG 18 1_555 B DA 4 8_555 B DT 19 1_555 B DA 3 8_555 1.002 -0.506 3.486 -0.013 -1.131 35.812 -0.649 -1.630 3.500 -1.838 0.021 35.829 17 WW_DG18DT19:DA3DA4_WW W 18 ? W 4 ? W 19 ? W 3 ? 1 B DT 19 1_555 B DA 3 8_555 B DA 20 1_555 B DG 2 8_555 -0.212 -0.131 3.134 3.633 2.014 33.602 -0.534 0.923 3.082 3.467 -6.254 33.851 18 WW_DT19DA20:DG2DA3_WW W 19 ? W 3 ? W 20 ? W 2 ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #