data_1KKM # _model_server_result.job_id TPXLdMeIhm2Dvr4kPCE9YQ _model_server_result.datetime_utc '2024-12-22 05:58:57' _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 1kkm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":502}' # _entry.id 1KKM # _exptl.entry_id 1KKM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 94.971 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHATE ION' _entity.pdbx_number_of_molecules 3 _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 1KKM _cell.length_a 80.832 _cell.length_b 80.832 _cell.length_c 252.488 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KKM _symmetry.cell_setting ? _symmetry.Int_Tables_number 153 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 1 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_and_software_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,Q,R _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _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[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_775 -y+2,-x+2,-z+1/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 80.832 140.005131 84.162667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 H N N ? 4 J N N ? 4 L N N # 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 covale ? covale1 D C LYS 57 H LYS 45 1_555 D CA SEP 58 H SEP 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? covale ? covale2 D C LYS 57 H LYS 45 1_555 D N SEP 58 H SEP 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.294 ? covale ? covale3 D C SEP 58 H SEP 46 1_555 D N ILE 59 H ILE 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.311 ? covale ? covale4 D CA SEP 58 H SEP 46 1_555 D N ILE 59 H ILE 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? covale ? covale5 E C LYS 57 I LYS 45 1_555 E N SEP 58 I SEP 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.574 ? covale ? covale6 E C SEP 58 I SEP 46 1_555 E N ILE 59 I ILE 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? covale ? covale7 F C LYS 57 J LYS 45 1_555 F N SEP 58 J SEP 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale8 F C SEP 58 J SEP 46 1_555 F N ILE 59 J ILE 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? metalc ? metalc1 A OG SER 48 A SER 162 1_555 G CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.879 ? metalc ? metalc2 A OE1 GLU 90 A GLU 204 1_555 G CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? metalc ? metalc3 A O GLU 90 A GLU 204 1_555 G CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? metalc ? metalc4 G CA CA . A CA 401 1_555 D O1P SEP 58 H SEP 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? metalc ? metalc5 B OG SER 48 B SER 162 1_555 I CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.839 ? metalc ? metalc6 B O GLU 90 B GLU 204 1_555 I CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.867 ? metalc ? metalc7 B OE1 GLU 90 B GLU 204 1_555 I CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? metalc ? metalc8 I CA CA . B CA 402 1_555 N O HOH . B HOH 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.974 ? metalc ? metalc9 I CA CA . B CA 402 1_555 E O1P SEP 58 I SEP 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? metalc ? metalc10 C OG SER 48 C SER 162 1_555 K CA CA . C CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.988 ? metalc ? metalc11 C OE1 GLU 90 C GLU 204 1_555 K CA CA . C CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc12 C O GLU 90 C GLU 204 1_555 K CA CA . C CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? metalc ? metalc13 K CA CA . C CA 403 1_555 L O3 PO4 . C PO4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.382 ? metalc ? metalc14 K CA CA . C CA 403 1_555 O O HOH . C HOH 543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc15 K CA CA . C CA 403 1_555 F O1P SEP 58 J SEP 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? # _chem_comp.formula 'O4 P -3' _chem_comp.formula_weight 94.971 _chem_comp.id PO4 _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHATE ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag P O1 PO4 doub 247 n n P O2 PO4 sing 248 n n P O3 PO4 sing 249 n n P O4 PO4 sing 250 n n # _atom_sites.entry_id 1KKM _atom_sites.fract_transf_matrix[1][1] 0.012371 _atom_sites.fract_transf_matrix[1][2] 0.007143 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014285 _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] 0.003961 _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 3 CA A 1 401 401 CA CA . H 4 PO4 A 1 501 402 PO4 PO4 . I 3 CA B 1 402 401 CA CA . J 4 PO4 B 1 502 402 PO4 PO4 . K 3 CA C 1 403 401 CA CA . L 4 PO4 C 1 503 402 PO4 PO4 . M 5 HOH A 1 502 4 HOH HOH . M 5 HOH A 2 503 5 HOH HOH . M 5 HOH A 3 504 6 HOH HOH . M 5 HOH A 4 505 7 HOH HOH . M 5 HOH A 5 506 8 HOH HOH . M 5 HOH A 6 507 19 HOH HOH . M 5 HOH A 7 508 20 HOH HOH . M 5 HOH A 8 509 21 HOH HOH . M 5 HOH A 9 510 23 HOH HOH . M 5 HOH A 10 511 24 HOH HOH . M 5 HOH A 11 512 35 HOH HOH . M 5 HOH A 12 513 36 HOH HOH . M 5 HOH A 13 514 37 HOH HOH . M 5 HOH A 14 515 38 HOH HOH . M 5 HOH A 15 516 39 HOH HOH . M 5 HOH A 16 517 40 HOH HOH . M 5 HOH A 17 518 41 HOH HOH . M 5 HOH A 18 519 42 HOH HOH . M 5 HOH A 19 520 47 HOH HOH . M 5 HOH A 20 521 48 HOH HOH . M 5 HOH A 21 522 49 HOH HOH . M 5 HOH A 22 523 50 HOH HOH . M 5 HOH A 23 524 51 HOH HOH . M 5 HOH A 24 525 52 HOH HOH . M 5 HOH A 25 526 53 HOH HOH . M 5 HOH A 26 527 56 HOH HOH . M 5 HOH A 27 528 57 HOH HOH . M 5 HOH A 28 529 62 HOH HOH . M 5 HOH A 29 530 63 HOH HOH . M 5 HOH A 30 531 66 HOH HOH . M 5 HOH A 31 532 107 HOH HOH . M 5 HOH A 32 533 129 HOH HOH . M 5 HOH A 33 534 130 HOH HOH . M 5 HOH A 34 535 131 HOH HOH . M 5 HOH A 35 536 133 HOH HOH . M 5 HOH A 36 537 145 HOH HOH . M 5 HOH A 37 538 146 HOH HOH . M 5 HOH A 38 539 152 HOH HOH . M 5 HOH A 39 540 156 HOH HOH . N 5 HOH B 1 503 1 HOH HOH . N 5 HOH B 2 504 9 HOH HOH . N 5 HOH B 3 505 14 HOH HOH . N 5 HOH B 4 506 15 HOH HOH . N 5 HOH B 5 507 18 HOH HOH . N 5 HOH B 6 508 26 HOH HOH . N 5 HOH B 7 509 32 HOH HOH . N 5 HOH B 8 510 34 HOH HOH . N 5 HOH B 9 511 45 HOH HOH . N 5 HOH B 10 512 46 HOH HOH . N 5 HOH B 11 513 64 HOH HOH . N 5 HOH B 12 514 65 HOH HOH . N 5 HOH B 13 515 68 HOH HOH . N 5 HOH B 14 516 69 HOH HOH . N 5 HOH B 15 517 70 HOH HOH . N 5 HOH B 16 518 73 HOH HOH . N 5 HOH B 17 519 74 HOH HOH . N 5 HOH B 18 520 75 HOH HOH . N 5 HOH B 19 521 76 HOH HOH . N 5 HOH B 20 522 77 HOH HOH . N 5 HOH B 21 523 78 HOH HOH . N 5 HOH B 22 524 79 HOH HOH . N 5 HOH B 23 525 80 HOH HOH . N 5 HOH B 24 526 81 HOH HOH . N 5 HOH B 25 527 106 HOH HOH . N 5 HOH B 26 528 109 HOH HOH . N 5 HOH B 27 529 111 HOH HOH . N 5 HOH B 28 530 112 HOH HOH . N 5 HOH B 29 531 113 HOH HOH . N 5 HOH B 30 532 114 HOH HOH . N 5 HOH B 31 533 121 HOH HOH . N 5 HOH B 32 534 122 HOH HOH . N 5 HOH B 33 535 139 HOH HOH . N 5 HOH B 34 536 140 HOH HOH . N 5 HOH B 35 537 141 HOH HOH . N 5 HOH B 36 538 142 HOH HOH . N 5 HOH B 37 539 147 HOH HOH . N 5 HOH B 38 540 149 HOH HOH . N 5 HOH B 39 541 151 HOH HOH . N 5 HOH B 40 542 153 HOH HOH . N 5 HOH B 41 543 154 HOH HOH . N 5 HOH B 42 544 155 HOH HOH . N 5 HOH B 43 545 158 HOH HOH . N 5 HOH B 44 546 159 HOH HOH . N 5 HOH B 45 547 160 HOH HOH . N 5 HOH B 46 548 168 HOH HOH . N 5 HOH B 47 549 169 HOH HOH . N 5 HOH B 48 550 403 HOH HOH . O 5 HOH C 1 504 16 HOH HOH . O 5 HOH C 2 505 17 HOH HOH . O 5 HOH C 3 506 22 HOH HOH . O 5 HOH C 4 507 25 HOH HOH . O 5 HOH C 5 508 28 HOH HOH . O 5 HOH C 6 509 29 HOH HOH . O 5 HOH C 7 510 30 HOH HOH . O 5 HOH C 8 511 31 HOH HOH . O 5 HOH C 9 512 43 HOH HOH . O 5 HOH C 10 513 44 HOH HOH . O 5 HOH C 11 514 54 HOH HOH . O 5 HOH C 12 515 58 HOH HOH . O 5 HOH C 13 516 59 HOH HOH . O 5 HOH C 14 517 60 HOH HOH . O 5 HOH C 15 518 61 HOH HOH . O 5 HOH C 16 519 71 HOH HOH . O 5 HOH C 17 520 72 HOH HOH . O 5 HOH C 18 521 82 HOH HOH . O 5 HOH C 19 522 83 HOH HOH . O 5 HOH C 20 523 84 HOH HOH . O 5 HOH C 21 524 85 HOH HOH . O 5 HOH C 22 525 86 HOH HOH . O 5 HOH C 23 526 87 HOH HOH . O 5 HOH C 24 527 88 HOH HOH . O 5 HOH C 25 528 104 HOH HOH . O 5 HOH C 26 529 108 HOH HOH . O 5 HOH C 27 530 110 HOH HOH . O 5 HOH C 28 531 115 HOH HOH . O 5 HOH C 29 532 116 HOH HOH . O 5 HOH C 30 533 117 HOH HOH . O 5 HOH C 31 534 118 HOH HOH . O 5 HOH C 32 535 128 HOH HOH . O 5 HOH C 33 536 132 HOH HOH . O 5 HOH C 34 537 143 HOH HOH . O 5 HOH C 35 538 150 HOH HOH . O 5 HOH C 36 539 157 HOH HOH . O 5 HOH C 37 540 163 HOH HOH . O 5 HOH C 38 541 164 HOH HOH . O 5 HOH C 39 542 167 HOH HOH . O 5 HOH C 40 543 403 HOH HOH . P 5 HOH H 1 89 10 HOH HOH . P 5 HOH H 2 90 11 HOH HOH . P 5 HOH H 3 91 12 HOH HOH . P 5 HOH H 4 92 13 HOH HOH . P 5 HOH H 5 93 89 HOH HOH . P 5 HOH H 6 94 90 HOH HOH . P 5 HOH H 7 95 91 HOH HOH . P 5 HOH H 8 96 92 HOH HOH . P 5 HOH H 9 97 119 HOH HOH . P 5 HOH H 10 98 123 HOH HOH . P 5 HOH H 11 99 134 HOH HOH . P 5 HOH H 12 100 135 HOH HOH . P 5 HOH H 13 101 161 HOH HOH . P 5 HOH H 14 102 162 HOH HOH . Q 5 HOH I 1 89 33 HOH HOH . Q 5 HOH I 2 90 55 HOH HOH . Q 5 HOH I 3 91 67 HOH HOH . Q 5 HOH I 4 92 93 HOH HOH . Q 5 HOH I 5 93 94 HOH HOH . Q 5 HOH I 6 94 95 HOH HOH . Q 5 HOH I 7 95 96 HOH HOH . Q 5 HOH I 8 96 97 HOH HOH . Q 5 HOH I 9 97 98 HOH HOH . Q 5 HOH I 10 98 124 HOH HOH . Q 5 HOH I 11 99 136 HOH HOH . Q 5 HOH I 12 100 148 HOH HOH . Q 5 HOH I 13 101 165 HOH HOH . Q 5 HOH I 14 102 166 HOH HOH . R 5 HOH J 1 89 2 HOH HOH . R 5 HOH J 2 90 3 HOH HOH . R 5 HOH J 3 91 27 HOH HOH . R 5 HOH J 4 92 99 HOH HOH . R 5 HOH J 5 93 100 HOH HOH . R 5 HOH J 6 94 101 HOH HOH . R 5 HOH J 7 95 102 HOH HOH . R 5 HOH J 8 96 103 HOH HOH . R 5 HOH J 9 97 105 HOH HOH . R 5 HOH J 10 98 120 HOH HOH . R 5 HOH J 11 99 125 HOH HOH . R 5 HOH J 12 100 126 HOH HOH . R 5 HOH J 13 101 127 HOH HOH . R 5 HOH J 14 102 137 HOH HOH . R 5 HOH J 15 103 138 HOH HOH . R 5 HOH J 16 104 144 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P P PO4 . . . J 4 46.352 79.196 17.315 0.75 39.29 ? P PO4 502 B 1 HETATM 2 O O1 PO4 . . . J 4 46.191 80.53 16.694 0 41.58 ? O1 PO4 502 B 1 HETATM 3 O O2 PO4 . . . J 4 47.471 78.486 16.664 0.75 42.93 ? O2 PO4 502 B 1 HETATM 4 O O3 PO4 . . . J 4 46.634 79.352 18.762 0.75 42.31 ? O3 PO4 502 B 1 HETATM 5 O O4 PO4 . . . J 4 45.101 78.417 17.141 0.75 43.01 ? O4 PO4 502 B 1 # _model_server_stats.io_time_ms 76 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 5 #