data_6KD5 # _model_server_result.job_id YQSNH55ZGUXKLu1KQAYXtA _model_server_result.datetime_utc '2024-11-30 07:31:20' _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 6kd5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":404}' # _entry.id 6KD5 # _exptl.entry_id 6KD5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _entity.pdbx_number_of_molecules 1 _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 90 _cell.entry_id 6KD5 _cell.length_a 55.84 _cell.length_b 62.4 _cell.length_c 171.63 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KD5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 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 ? 4 2 1 FUC NAG C1 O1 . O6 HO6 . sing 2 ? 5 2 1 NAG 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 4 n D NAG 1 D 1 NAG A 801 NAG 4 n D FUC 2 D 2 FUC A 802 FUC 5 n E NAG 1 E 1 NAG B 811 NAG 5 n E NAG 2 E 2 NAG B 812 NAG # 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 35 A CYS 204 1_555 A SG CYS 48 A CYS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 A SG CYS 42 A CYS 211 1_555 A SG CYS 57 A CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 81 A CYS 250 1_555 A SG CYS 135 A CYS 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf4 A SG CYS 94 A CYS 263 1_555 A SG CYS 145 A CYS 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf5 A SG CYS 148 A CYS 317 1_555 B SG CYS 109 B CYS 434 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf6 B SG CYS 26 B CYS 351 1_555 B SG CYS 42 B CYS 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf7 B SG CYS 123 B CYS 448 1_555 B SG CYS 192 B CYS 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf8 B SG CYS 155 B CYS 480 1_555 B SG CYS 171 B CYS 496 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 B SG CYS 182 B CYS 507 1_555 B SG CYS 210 B CYS 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? covale ? covale1 A ND2 ASN 86 A ASN 255 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 B NE2 HIS 41 B HIS 366 1_555 C C1 0QE 6 C 0QE 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.279 ? covale ? covale3 B ND2 ASN 80 B ASN 405 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale4 B OG SER 186 B SER 511 1_555 C C AR7 5 C AR7 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale5 C C1 DKA 1 C DKA 1 1_555 C N ARG 2 C ARG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 C C LYS 4 C LYS 4 1_555 C N AR7 5 C AR7 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.379 ? covale ? covale7 C C AR7 5 C AR7 5 1_555 C C1 0QE 6 C 0QE 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.544 ? covale ? covale8 D O6 NAG . D NAG 1 1_555 D C1 FUC . D FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? metalc ? metalc1 A O VAL 40 A VAL 209 1_555 I CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc2 A OD1 ASP 43 A ASP 212 1_555 I CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc3 A O VAL 45 A VAL 214 1_555 I CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc4 A OD2 ASP 47 A ASP 216 1_555 I CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc5 A OD2 ASP 53 A ASP 222 1_555 I CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc6 A OE2 GLU 54 A GLU 223 1_555 I CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? # _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 6KD5 _atom_sites.fract_transf_matrix[1][1] 0.017908 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016026 _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] 0.005826 _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 F 6 SO4 A 1 401 3 SO4 SO4 . G 6 SO4 A 1 402 5 SO4 SO4 . H 6 SO4 A 1 403 7 SO4 SO4 . I 7 CA A 1 404 11 CA CA . J 6 SO4 B 1 601 1 SO4 SO4 . K 6 SO4 B 1 602 4 SO4 SO4 . L 6 SO4 B 1 603 6 SO4 SO4 . M 6 SO4 C 1 101 2 SO4 SO4 . N 8 HOH A 1 501 50 HOH HOH . N 8 HOH A 2 502 9 HOH HOH . N 8 HOH A 3 503 68 HOH HOH . N 8 HOH A 4 504 79 HOH HOH . N 8 HOH A 5 505 45 HOH HOH . N 8 HOH A 6 506 31 HOH HOH . N 8 HOH A 7 507 55 HOH HOH . N 8 HOH A 8 508 23 HOH HOH . N 8 HOH A 9 509 34 HOH HOH . N 8 HOH A 10 510 72 HOH HOH . N 8 HOH A 11 511 5 HOH HOH . N 8 HOH A 12 512 37 HOH HOH . N 8 HOH A 13 513 25 HOH HOH . N 8 HOH A 14 514 71 HOH HOH . N 8 HOH A 15 515 44 HOH HOH . N 8 HOH A 16 516 38 HOH HOH . N 8 HOH A 17 517 11 HOH HOH . N 8 HOH A 18 518 30 HOH HOH . N 8 HOH A 19 519 6 HOH HOH . N 8 HOH A 20 520 22 HOH HOH . N 8 HOH A 21 521 29 HOH HOH . N 8 HOH A 22 522 17 HOH HOH . N 8 HOH A 23 523 42 HOH HOH . N 8 HOH A 24 524 56 HOH HOH . N 8 HOH A 25 525 10 HOH HOH . N 8 HOH A 26 526 65 HOH HOH . N 8 HOH A 27 527 81 HOH HOH . N 8 HOH A 28 528 66 HOH HOH . O 8 HOH B 1 701 36 HOH HOH . O 8 HOH B 2 702 35 HOH HOH . O 8 HOH B 3 703 19 HOH HOH . O 8 HOH B 4 704 1 HOH HOH . O 8 HOH B 5 705 4 HOH HOH . O 8 HOH B 6 706 26 HOH HOH . O 8 HOH B 7 707 16 HOH HOH . O 8 HOH B 8 708 39 HOH HOH . O 8 HOH B 9 709 58 HOH HOH . O 8 HOH B 10 710 75 HOH HOH . O 8 HOH B 11 711 27 HOH HOH . O 8 HOH B 12 712 14 HOH HOH . O 8 HOH B 13 713 48 HOH HOH . O 8 HOH B 14 714 15 HOH HOH . O 8 HOH B 15 715 61 HOH HOH . O 8 HOH B 16 716 67 HOH HOH . O 8 HOH B 17 717 24 HOH HOH . O 8 HOH B 18 718 51 HOH HOH . O 8 HOH B 19 719 74 HOH HOH . O 8 HOH B 20 720 7 HOH HOH . O 8 HOH B 21 721 70 HOH HOH . O 8 HOH B 22 722 53 HOH HOH . O 8 HOH B 23 723 32 HOH HOH . O 8 HOH B 24 724 13 HOH HOH . O 8 HOH B 25 725 43 HOH HOH . O 8 HOH B 26 726 3 HOH HOH . O 8 HOH B 27 727 18 HOH HOH . O 8 HOH B 28 728 77 HOH HOH . O 8 HOH B 29 729 76 HOH HOH . O 8 HOH B 30 730 80 HOH HOH . O 8 HOH B 31 731 21 HOH HOH . O 8 HOH B 32 732 28 HOH HOH . O 8 HOH B 33 733 2 HOH HOH . O 8 HOH B 34 734 20 HOH HOH . O 8 HOH B 35 735 54 HOH HOH . O 8 HOH B 36 736 49 HOH HOH . O 8 HOH B 37 737 46 HOH HOH . O 8 HOH B 38 738 8 HOH HOH . O 8 HOH B 39 739 47 HOH HOH . O 8 HOH B 40 740 41 HOH HOH . O 8 HOH B 41 741 52 HOH HOH . O 8 HOH B 42 742 73 HOH HOH . O 8 HOH B 43 743 33 HOH HOH . O 8 HOH B 44 744 12 HOH HOH . O 8 HOH B 45 745 78 HOH HOH . O 8 HOH B 46 746 62 HOH HOH . O 8 HOH B 47 747 40 HOH HOH . O 8 HOH B 48 748 69 HOH HOH . O 8 HOH B 49 749 63 HOH HOH . O 8 HOH B 50 750 64 HOH HOH . O 8 HOH B 51 751 59 HOH HOH . O 8 HOH B 52 752 57 HOH HOH . O 8 HOH B 53 753 60 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 I _atom_site.label_entity_id 7 _atom_site.Cartn_x -3.523 _atom_site.Cartn_y -8.398 _atom_site.Cartn_z -36.096 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 30.1 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 404 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 216 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #