data_1DVA # _model_server_result.job_id N17tVrgXluuAJ5X9qrdFXg _model_server_result.datetime_utc '2024-11-02 07:31:19' _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 1dva # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":302}' # _entry.id 1DVA # _exptl.entry_id 1DVA _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 99.48 _cell.angle_gamma 90 _cell.entry_id 1DVA _cell.length_a 70.49 _cell.length_b 55.26 _cell.length_c 111.73 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DVA _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,B,C,G,H,I,J,K,L,M,T 1 1 D,E,F,N,O,P,Q,R,S,U 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 I N N ? 6 M N N ? 6 O N N ? 6 S N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 GAL _pdbx_entity_branch_link.comp_id_2 BGC _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 4 n G BGC 1 A 1 BGC L 52 GLC 4 n G GAL 2 A 2 GAL L 52 GAL # 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 7 H CYS 22 1_555 A SG CYS 12 H CYS 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 26 H CYS 42 1_555 A SG CYS 42 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 A SG CYS 110 H CYS 122 1_555 B SG CYS 94 L CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 A SG CYS 158 H CYS 168 1_555 A SG CYS 177 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf5 A SG CYS 188 H CYS 191 1_555 A SG CYS 216 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf6 B SG CYS 9 L CYS 50 1_555 B SG CYS 20 L CYS 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf7 B SG CYS 14 L CYS 55 1_555 B SG CYS 29 L CYS 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf8 B SG CYS 31 L CYS 72 1_555 B SG CYS 40 L CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf9 B SG CYS 50 L CYS 91 1_555 B SG CYS 61 L CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 B SG CYS 57 L CYS 98 1_555 B SG CYS 71 L CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf11 B SG CYS 73 L CYS 114 1_555 B SG CYS 86 L CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf12 C SG CYS 4 X CYS 3 1_555 C SG CYS 14 X CYS 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf13 D SG CYS 7 I CYS 22 1_555 D SG CYS 12 I CYS 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf14 D SG CYS 26 I CYS 42 1_555 D SG CYS 42 I CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf15 D SG CYS 110 I CYS 122 1_555 E SG CYS 94 M CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf16 D SG CYS 158 I CYS 168 1_555 D SG CYS 177 I CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf17 D SG CYS 188 I CYS 191 1_555 D SG CYS 216 I CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf18 E SG CYS 9 M CYS 50 1_555 E SG CYS 20 M CYS 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf19 E SG CYS 14 M CYS 55 1_555 E SG CYS 29 M CYS 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf20 E SG CYS 31 M CYS 72 1_555 E SG CYS 40 M CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf21 E SG CYS 50 M CYS 91 1_555 E SG CYS 61 M CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf22 E SG CYS 57 M CYS 98 1_555 E SG CYS 71 M CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf23 E SG CYS 73 M CYS 114 1_555 E SG CYS 86 M CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf24 F SG CYS 4 Y CYS 3 1_555 F SG CYS 14 Y CYS 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? covale ? covale1 H C3 0Z6 . H 0Z6 1 1_555 A NE2 HIS 41 H HIS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.499 ? covale ? covale2 H C2 0Z6 . H 0Z6 1 1_555 A OG SER 192 H SER 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale3 B OG SER 11 L SER 52 1_555 G C1 BGC . A BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale4 B OG SER 19 L SER 60 1_555 K C1 FUC . L FUC 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? covale ? covale5 C C ACE 1 X ACE 0 1_555 C N ALA 2 X ALA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale6 N C3 0Z6 . I 0Z6 1 1_555 D NE2 HIS 41 I HIS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.501 ? covale ? covale7 N C2 0Z6 . I 0Z6 1 1_555 D OG SER 192 I SER 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale8 E OG SER 11 M SER 52 1_555 Q C1 GLC . M GLC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale9 E OG SER 19 M SER 60 1_555 R C1 FUL . M FUL 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale10 F C ACE 1 Y ACE 0 1_555 F N ALA 2 Y ALA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale11 G O4 BGC . A BGC 1 1_555 G C1 GAL . A GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? metalc ? metalc1 A OE1 GLU 58 H GLU 70 1_555 I CA CA . H CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.006 ? metalc ? metalc2 A O ASP 60 H ASP 72 1_555 I CA CA . H CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc3 A O GLU 63 H GLU 75 1_555 I CA CA . H CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc4 A OD1 ASP 65 H ASP 77 1_555 I CA CA . H CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.903 ? metalc ? metalc5 A OE2 GLU 68 H GLU 80 1_555 I CA CA . H CA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.135 ? metalc ? metalc6 I CA CA . H CA 300 1_555 T O HOH . H HOH 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc7 B OD2 ASP 5 L ASP 46 1_555 M CA CA . L CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.99 ? metalc ? metalc8 B O GLY 6 L GLY 47 1_555 M CA CA . L CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc9 B OE1 GLN 8 L GLN 49 1_555 M CA CA . L CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.065 ? metalc ? metalc10 B OD2 ASP 22 L ASP 63 1_555 M CA CA . L CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc11 B OD1 ASP 22 L ASP 63 1_555 M CA CA . L CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? metalc ? metalc12 B O GLN 23 L GLN 64 1_555 M CA CA . L CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? metalc ? metalc13 D OE1 GLU 58 I GLU 70 1_555 O CA CA . I CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.924 ? metalc ? metalc14 D O ASP 60 I ASP 72 1_555 O CA CA . I CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc15 D O GLU 63 I GLU 75 1_555 O CA CA . I CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc16 D OD1 ASP 65 I ASP 77 1_555 O CA CA . I CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.894 ? metalc ? metalc17 D OE2 GLU 68 I GLU 80 1_555 O CA CA . I CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.993 ? metalc ? metalc18 E OD2 ASP 5 M ASP 46 1_555 S CA CA . M CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.042 ? metalc ? metalc19 E O GLY 6 M GLY 47 1_555 S CA CA . M CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc20 E OE1 GLN 8 M GLN 49 1_555 S CA CA . M CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.098 ? metalc ? metalc21 E OD1 ASP 22 M ASP 63 1_555 S CA CA . M CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc22 E OD2 ASP 22 M ASP 63 1_555 S CA CA . M CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc23 E O GLN 23 M GLN 64 1_555 S CA CA . M CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? # _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 1DVA _atom_sites.fract_transf_matrix[1][1] 0.014186 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002369 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018096 _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] 0.009074 _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 H 5 0Z6 H 1 1 1 0Z6 DPN . I 6 CA H 1 300 300 CA CA . J 7 CAC H 1 310 286 CAC CAC . K 8 FUC L 1 504 60 FUC FUC . L 8 FUC L 1 506 52 FUC FUC . M 6 CA L 1 302 300 CA CA . N 5 0Z6 I 1 1 1 0Z6 DPN . O 6 CA I 1 301 300 CA CA . P 7 CAC I 1 311 286 CAC CAC . Q 9 GLC M 1 503 52 GLC GLC . R 10 FUL M 1 505 60 FUL FUC . S 6 CA M 1 303 300 CA CA . T 11 HOH H 1 400 400 HOH HOH . T 11 HOH H 2 401 401 HOH HOH . T 11 HOH H 3 402 402 HOH HOH . U 11 HOH I 1 403 400 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 M _atom_site.label_entity_id 6 _atom_site.Cartn_x -23.05 _atom_site.Cartn_y 20.418 _atom_site.Cartn_z 34.314 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 72.48 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 302 _atom_site.auth_asym_id L _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 238 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #