data_4NYT # _model_server_result.job_id kdCEg4-2SMxS7-5nMuIoDg _model_server_result.datetime_utc '2024-11-23 19:59:25' _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 4nyt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":305}' # _entry.id 4NYT # _exptl.entry_id 4NYT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 4 _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 90 _cell.angle_gamma 120 _cell.entry_id 4NYT _cell.length_a 96.13 _cell.length_b 96.13 _cell.length_c 139.88 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NYT _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 4 F N N ? 4 K N N ? 4 L N N ? 4 M N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type 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 MAN NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 1 FUC NAG C1 O1 . O6 HO6 . 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 D NAG 1 D 1 NAG C 1001 NAG 2 n D NAG 2 D 2 NAG C 1002 NAG 2 n D MAN 3 D 3 MAN C 1003 MAN 2 n D FUC 4 D 4 FUC C 1004 FUC # 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 2 C CYS 73 1_555 A SG CYS 30 C CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? disulf ? disulf2 A SG CYS 9 C CYS 80 1_555 A SG CYS 37 C CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf3 A SG CYS 161 C CYS 232 1_555 A SG CYS 174 C CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? disulf ? disulf4 B SG CYS 9 A CYS 80 1_555 B SG CYS 37 A CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? disulf ? disulf5 B SG CYS 161 A CYS 232 1_555 B SG CYS 174 A CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf6 C SG CYS 9 B CYS 80 1_555 C SG CYS 37 B CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf7 C SG CYS 161 B CYS 232 1_555 C SG CYS 174 B CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? covale ? covale1 A ND2 ASN 144 C ASN 215 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale2 B ND2 ASN 144 A ASN 215 1_555 I C1 NAG . A NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale4 D O6 NAG . D NAG 1 1_555 D C1 FUC . D FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale5 D O4 NAG . D NAG 2 1_555 D C1 MAN . D MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? metalc ? metalc1 A OD2 ASP 153 C ASP 224 1_555 F CA CA . C CA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc2 A OD1 ASP 153 C ASP 224 1_555 F CA CA . C CA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc3 A OD1 ASP 155 C ASP 226 1_555 F CA CA . C CA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc4 A O ASN 157 C ASN 228 1_555 F CA CA . C CA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc5 A O GLY 159 C GLY 230 1_555 F CA CA . C CA 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc6 F CA CA . C CA 306 1_555 N O HOH . C HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc7 F CA CA . C CA 306 1_555 N O HOH . C HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc8 B O ASP 151 A ASP 222 1_555 L CA CA . A CA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc9 B OD2 ASP 153 A ASP 224 1_555 K CA CA . A CA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc10 B OD1 ASP 153 A ASP 224 1_555 K CA CA . A CA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc11 B OD1 ASP 155 A ASP 226 1_555 K CA CA . A CA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc12 B O ASN 157 A ASN 228 1_555 K CA CA . A CA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc13 B O GLY 159 A GLY 230 1_555 K CA CA . A CA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc14 K CA CA . A CA 304 1_555 O O HOH . A HOH 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc15 L CA CA . A CA 305 1_555 O O HOH . A HOH 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc16 C OD2 ASP 153 B ASP 224 1_555 M CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc17 C OD1 ASP 153 B ASP 224 1_555 M CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.019 ? metalc ? metalc18 C OD1 ASP 155 B ASP 226 1_555 M CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.786 ? metalc ? metalc19 C O ASP 155 B ASP 226 1_555 M CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.137 ? metalc ? metalc20 C O ASN 157 B ASN 228 1_555 M CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc21 C O GLY 159 B GLY 230 1_555 M CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.648 ? # _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 4NYT _atom_sites.fract_transf_matrix[1][1] 0.010403 _atom_sites.fract_transf_matrix[1][2] 0.006006 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012012 _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] 0.007149 _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 E 3 ACT C 1 301 1290 ACT ACT . F 4 CA C 1 306 1 CA CA . G 5 PO4 C 1 307 4 PO4 PO4 . H 3 ACT A 1 301 1290 ACT ACT . I 6 NAG A 1 302 1001 NAG NAG . J 7 PC A 1 303 3 PC PC . K 4 CA A 1 304 1 CA CA . L 4 CA A 1 305 2 CA CA . M 4 CA B 1 301 1 CA CA . N 8 HOH C 1 401 1 HOH HOH . N 8 HOH C 2 402 2 HOH HOH . N 8 HOH C 3 403 4 HOH HOH . N 8 HOH C 4 404 5 HOH HOH . N 8 HOH C 5 405 6 HOH HOH . N 8 HOH C 6 406 7 HOH HOH . N 8 HOH C 7 407 8 HOH HOH . N 8 HOH C 8 408 9 HOH HOH . N 8 HOH C 9 409 10 HOH HOH . N 8 HOH C 10 410 11 HOH HOH . N 8 HOH C 11 411 12 HOH HOH . N 8 HOH C 12 412 13 HOH HOH . N 8 HOH C 13 413 14 HOH HOH . N 8 HOH C 14 414 15 HOH HOH . N 8 HOH C 15 415 24 HOH HOH . N 8 HOH C 16 416 25 HOH HOH . N 8 HOH C 17 417 29 HOH HOH . N 8 HOH C 18 418 32 HOH HOH . N 8 HOH C 19 419 36 HOH HOH . N 8 HOH C 20 420 38 HOH HOH . N 8 HOH C 21 421 41 HOH HOH . N 8 HOH C 22 422 42 HOH HOH . N 8 HOH C 23 423 43 HOH HOH . N 8 HOH C 24 424 44 HOH HOH . N 8 HOH C 25 425 45 HOH HOH . N 8 HOH C 26 426 46 HOH HOH . N 8 HOH C 27 427 47 HOH HOH . N 8 HOH C 28 428 48 HOH HOH . N 8 HOH C 29 429 49 HOH HOH . N 8 HOH C 30 430 50 HOH HOH . N 8 HOH C 31 431 51 HOH HOH . N 8 HOH C 32 432 61 HOH HOH . N 8 HOH C 33 433 73 HOH HOH . O 8 HOH A 1 401 3 HOH HOH . O 8 HOH A 2 402 16 HOH HOH . O 8 HOH A 3 403 17 HOH HOH . O 8 HOH A 4 404 18 HOH HOH . O 8 HOH A 5 405 19 HOH HOH . O 8 HOH A 6 406 22 HOH HOH . O 8 HOH A 7 407 23 HOH HOH . O 8 HOH A 8 408 26 HOH HOH . O 8 HOH A 9 409 27 HOH HOH . O 8 HOH A 10 410 28 HOH HOH . O 8 HOH A 11 411 30 HOH HOH . O 8 HOH A 12 412 31 HOH HOH . O 8 HOH A 13 413 33 HOH HOH . O 8 HOH A 14 414 34 HOH HOH . O 8 HOH A 15 415 35 HOH HOH . O 8 HOH A 16 416 39 HOH HOH . O 8 HOH A 17 417 40 HOH HOH . O 8 HOH A 18 418 52 HOH HOH . O 8 HOH A 19 419 53 HOH HOH . O 8 HOH A 20 420 54 HOH HOH . O 8 HOH A 21 421 55 HOH HOH . O 8 HOH A 22 422 56 HOH HOH . O 8 HOH A 23 423 57 HOH HOH . O 8 HOH A 24 424 58 HOH HOH . O 8 HOH A 25 425 60 HOH HOH . O 8 HOH A 26 426 62 HOH HOH . O 8 HOH A 27 427 63 HOH HOH . O 8 HOH A 28 428 65 HOH HOH . O 8 HOH A 29 429 66 HOH HOH . O 8 HOH A 30 430 67 HOH HOH . O 8 HOH A 31 431 68 HOH HOH . O 8 HOH A 32 432 69 HOH HOH . O 8 HOH A 33 433 70 HOH HOH . O 8 HOH A 34 434 72 HOH HOH . P 8 HOH B 1 401 20 HOH HOH . P 8 HOH B 2 402 64 HOH HOH . P 8 HOH B 3 403 71 HOH HOH . # _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 L _atom_site.label_entity_id 4 _atom_site.Cartn_x 21.298 _atom_site.Cartn_y -63.945 _atom_site.Cartn_z 21.037 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 46.64 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 305 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 415 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #