data_7LYU # _model_server_result.job_id ytLWP3qZ4sLsASZ-Icy_YA _model_server_result.datetime_utc '2024-11-24 20:09:22' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 7lyu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":3502}' # _entry.id 7LYU # _exptl.entry_id 7LYU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 104.109 _cell.angle_gamma 90 _cell.entry_id 7LYU _cell.length_a 60.171 _cell.length_b 104.059 _cell.length_c 67.615 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7LYU _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G,H 1 1 B,E,F,I,J 2 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 G N N ? 6 H N N ? 6 I N N ? 6 J N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 oligosaccharide 5 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 2 5 4 MAN MAN C1 O1 . O3 HO3 . sing 5 ? 2 6 3 MAN BMA C1 O1 . O3 HO3 . sing 6 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 7 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 8 ? 3 4 3 MAN BMA C1 O1 . O6 HO6 . sing 9 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 10 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 11 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . sing 12 ? 4 5 4 MAN MAN C1 O1 . O2 HO2 . sing 13 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 14 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C NAG 1 C 1 NAG A 3437 NAG 2 n C NAG 2 C 2 NAG A 3438 NAG 2 n C BMA 3 C 3 BMA A 3439 BMA 2 n C MAN 4 C 4 MAN A 3440 MAN 2 n C MAN 5 C 5 MAN A 3441 MAN 2 n C MAN 6 C 6 MAN A 3442 MAN 3 n D NAG 1 D 1 NAG A 3443 NAG 3 n D NAG 2 D 2 NAG A 3444 NAG 3 n D BMA 3 D 3 BMA A 3445 BMA 3 n D MAN 4 D 4 MAN A 3446 MAN 4 n E NAG 1 E 1 NAG B 3437 NAG 4 n E NAG 2 E 2 NAG B 3438 NAG 4 n E BMA 3 E 3 BMA B 3439 BMA 4 n E MAN 4 E 4 MAN B 3440 MAN 4 n E MAN 5 E 5 MAN B 3441 MAN 5 n F NAG 1 F 1 NAG B 3442 NAG 5 n F NAG 2 F 2 NAG B 3443 NAG 5 n F BMA 3 F 3 BMA B 3444 BMA # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 46 A CYS 3087 1_555 A SG CYS 88 A CYS 3129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 93 A CYS 3134 1_555 A SG CYS 272 A CYS 3313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 119 A CYS 3160 1_555 A SG CYS 129 A CYS 3170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 191 A CYS 3232 1_555 A SG CYS 201 A CYS 3242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 195 A CYS 3236 1_555 A SG CYS 207 A CYS 3248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf6 A SG CYS 209 A CYS 3250 1_555 A SG CYS 218 A CYS 3259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 A SG CYS 255 A CYS 3296 1_555 A SG CYS 305 A CYS 3346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf8 B SG CYS 46 B CYS 3087 1_555 B SG CYS 88 B CYS 3129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 B SG CYS 93 B CYS 3134 1_555 B SG CYS 272 B CYS 3313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf10 B SG CYS 119 B CYS 3160 1_555 B SG CYS 129 B CYS 3170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 B SG CYS 191 B CYS 3232 1_555 B SG CYS 201 B CYS 3242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? disulf ? disulf12 B SG CYS 195 B CYS 3236 1_555 B SG CYS 207 B CYS 3248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf13 B SG CYS 209 B CYS 3250 1_555 B SG CYS 218 B CYS 3259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf14 B SG CYS 255 B CYS 3296 1_555 B SG CYS 305 B CYS 3346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 A ND2 ASN 144 A ASN 3185 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 A ND2 ASN 371 A ASN 3412 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale3 B ND2 ASN 144 B ASN 3185 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 B ND2 ASN 371 B ASN 3412 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale7 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale8 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale9 C O3 MAN . C MAN 4 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.472 ? covale ? covale11 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale12 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale13 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale14 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale15 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale16 E O2 MAN . E MAN 4 1_555 E C1 MAN . E MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale17 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale18 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? metalc ? metalc1 A O THR 21 A THR 3062 1_555 G CA CA . A CA 3501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc2 A OG SER 50 A SER 3091 1_555 G CA CA . A CA 3501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc3 A OD1 ASP 183 A ASP 3224 1_555 G CA CA . A CA 3501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc4 A OD2 ASP 183 A ASP 3224 1_555 G CA CA . A CA 3501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.196 ? metalc ? metalc5 A O ASN 232 A ASN 3273 1_555 H CA CA . A CA 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc6 A O HIS 263 A HIS 3304 1_555 H CA CA . A CA 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc7 A O ASP 265 A ASP 3306 1_555 H CA CA . A CA 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.023 ? metalc ? metalc8 A OD1 ASP 381 A ASP 3422 1_555 H CA CA . A CA 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? metalc ? metalc9 A OD2 ASP 381 A ASP 3422 1_555 H CA CA . A CA 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc10 B O THR 21 B THR 3062 1_555 J CA CA . B CA 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc11 B OG SER 50 B SER 3091 1_555 J CA CA . B CA 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc12 B O PHE 51 B PHE 3092 1_555 J CA CA . B CA 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.91 ? metalc ? metalc13 B OD1 ASP 183 B ASP 3224 1_555 J CA CA . B CA 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc14 B OD2 ASP 183 B ASP 3224 1_555 J CA CA . B CA 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? metalc ? metalc15 B O HIS 263 B HIS 3304 1_555 I CA CA . B CA 3501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc16 B O ASP 265 B ASP 3306 1_555 I CA CA . B CA 3501 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.624 ? metalc ? metalc17 B O ASP 265 B ASP 3306 1_555 I CA CA . B CA 3501 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.624 ? metalc ? metalc18 B OD1 ASP 381 B ASP 3422 1_555 I CA CA . B CA 3501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.588 ? metalc ? metalc19 B OD2 ASP 381 B ASP 3422 1_555 I CA CA . B CA 3501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? # _chem_comp.formula 'Ca 2' _chem_comp.formula_weight 40.078 _chem_comp.id CA _chem_comp.mon_nstd_flag . _chem_comp.name 'CALCIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 7LYU _atom_sites.fract_transf_matrix[1][1] 0.016619 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004177 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00961 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.01525 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code G 6 CA A 1 3501 3449 CA CA . H 6 CA A 1 3502 3450 CA CA . I 6 CA B 1 3501 3449 CA CA . J 6 CA B 1 3502 3450 CA CA . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CA _atom_site.label_atom_id CA _atom_site.label_comp_id CA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id J _atom_site.label_entity_id 6 _atom_site.Cartn_x 26.284 _atom_site.Cartn_y 35.763 _atom_site.Cartn_z -0.674 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 74.1 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 3502 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 40 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 1 #