data_5SVK # _model_server_result.job_id 4C8ndPH3d7rx_qpPNh2Zbg _model_server_result.datetime_utc '2024-11-04 22:43:31' _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 5svk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":401}' # _entry.id 5SVK # _exptl.entry_id 5SVK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 5SVK _cell.length_a 173.15 _cell.length_b 173.15 _cell.length_c 173.15 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SVK _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 3' # 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,C,D,G,H,I,J,K,L,M,S 1 1,2,4 B,E,F,N,O,P,Q,R,T 2 1,3,5 # 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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 6_577 z+1/2,-x+5/2,-y+2 0 0 1 -1 0 0 0 -1 0 86.575 432.875 346.3 4 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 5 'crystal symmetry operation' 12_774 -y+5/2,-z+2,x-1/2 0 -1 0 0 0 -1 1 0 0 432.875 346.3 -86.575 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 G N N ? 3 N N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 GLC _pdbx_entity_branch_link.comp_id_2 GLC _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 2 n C GLC 1 C 1 GLC A 504 MAL 2 n C GLC 2 C 2 GLC A 504 MAL 2 n D GLC 1 D 1 GLC J 2 MAL 2 n D GLC 2 D 2 GLC J 2 MAL 2 n E GLC 1 E 1 GLC B 503 MAL 2 n E GLC 2 E 2 GLC B 503 MAL 2 n F GLC 1 F 1 GLC J 1 MAL 2 n F GLC 2 F 2 GLC J 1 MAL # 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 106 A CYS 107 1_555 A SG CYS 152 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 115 A CYS 116 1_555 A SG CYS 136 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 121 A CYS 122 1_555 A SG CYS 146 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 A SG CYS 202 A CYS 203 1_555 A SG CYS 212 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 A SG CYS 246 A CYS 247 1_555 A SG CYS 255 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 B SG CYS 106 B CYS 107 1_555 B SG CYS 152 B CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf7 B SG CYS 115 B CYS 116 1_555 B SG CYS 136 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 B SG CYS 121 B CYS 122 1_555 B SG CYS 146 B CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 B SG CYS 202 B CYS 203 1_555 B SG CYS 212 B CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf10 B SG CYS 246 B CYS 247 1_555 B SG CYS 255 B CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 138 A ASN 139 1_555 K C1 NAG . A NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 A ND2 ASN 169 A ASN 170 1_555 H C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale3 A ND2 ASN 193 A ASN 194 1_555 I C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale4 A ND2 ASN 289 A ASN 290 1_555 J C1 NAG . A NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 B ND2 ASN 169 B ASN 170 1_555 O C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale6 B ND2 ASN 193 B ASN 194 1_555 P C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale7 B ND2 ASN 289 B ASN 290 1_555 Q C1 NAG . B NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale8 C O4 GLC . C GLC 1 1_555 C C1 GLC . C GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 sing covale ? covale9 D O4 GLC . D GLC 1 1_555 D C1 GLC . D GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 sing covale ? covale10 E O4 GLC . E GLC 1 1_555 E C1 GLC . E GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 sing covale ? covale11 F O4 GLC . F GLC 1 1_555 F C1 GLC . F GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 sing # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5SVK _atom_sites.fract_transf_matrix[1][1] 0.005775 _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] 0.005775 _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] 0.005775 _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 ATP A 1 401 402 ATP ATP . H 4 NAG A 1 402 500 NAG NAG . I 4 NAG A 1 403 501 NAG NAG . J 4 NAG A 1 404 502 NAG NAG . K 4 NAG A 1 405 503 NAG NAG . L 5 EDO A 1 408 1 EDO EDO . M 6 MHA A 1 409 1 MHA LIG . N 3 ATP B 1 401 402 ATP ATP . O 4 NAG B 1 402 500 NAG NAG . P 4 NAG B 1 403 501 NAG NAG . Q 4 NAG B 1 404 502 NAG NAG . R 5 EDO B 1 407 2 EDO EDO . S 7 HOH A 1 501 33 HOH HOH . S 7 HOH A 2 502 60 HOH HOH . S 7 HOH A 3 503 23 HOH HOH . S 7 HOH A 4 504 22 HOH HOH . S 7 HOH A 5 505 8 HOH HOH . S 7 HOH A 6 506 1 HOH HOH . S 7 HOH A 7 507 55 HOH HOH . S 7 HOH A 8 508 4 HOH HOH . S 7 HOH A 9 509 81 HOH HOH . S 7 HOH A 10 510 64 HOH HOH . S 7 HOH A 11 511 12 HOH HOH . S 7 HOH A 12 512 27 HOH HOH . S 7 HOH A 13 513 34 HOH HOH . S 7 HOH A 14 514 17 HOH HOH . S 7 HOH A 15 515 53 HOH HOH . S 7 HOH A 16 516 14 HOH HOH . S 7 HOH A 17 517 68 HOH HOH . S 7 HOH A 18 518 5 HOH HOH . S 7 HOH A 19 519 13 HOH HOH . S 7 HOH A 20 520 16 HOH HOH . S 7 HOH A 21 521 56 HOH HOH . S 7 HOH A 22 522 28 HOH HOH . S 7 HOH A 23 523 26 HOH HOH . S 7 HOH A 24 524 31 HOH HOH . S 7 HOH A 25 525 9 HOH HOH . S 7 HOH A 26 526 80 HOH HOH . S 7 HOH A 27 527 3 HOH HOH . S 7 HOH A 28 528 32 HOH HOH . S 7 HOH A 29 529 20 HOH HOH . S 7 HOH A 30 530 6 HOH HOH . S 7 HOH A 31 531 57 HOH HOH . S 7 HOH A 32 532 10 HOH HOH . S 7 HOH A 33 533 62 HOH HOH . S 7 HOH A 34 534 7 HOH HOH . S 7 HOH A 35 535 71 HOH HOH . S 7 HOH A 36 536 19 HOH HOH . S 7 HOH A 37 537 70 HOH HOH . S 7 HOH A 38 538 54 HOH HOH . S 7 HOH A 39 539 11 HOH HOH . T 7 HOH B 1 501 66 HOH HOH . T 7 HOH B 2 502 75 HOH HOH . T 7 HOH B 3 503 36 HOH HOH . T 7 HOH B 4 504 47 HOH HOH . T 7 HOH B 5 505 45 HOH HOH . T 7 HOH B 6 506 42 HOH HOH . T 7 HOH B 7 507 82 HOH HOH . T 7 HOH B 8 508 46 HOH HOH . T 7 HOH B 9 509 41 HOH HOH . T 7 HOH B 10 510 39 HOH HOH . T 7 HOH B 11 511 61 HOH HOH . T 7 HOH B 12 512 63 HOH HOH . T 7 HOH B 13 513 49 HOH HOH . T 7 HOH B 14 514 67 HOH HOH . T 7 HOH B 15 515 74 HOH HOH . T 7 HOH B 16 516 59 HOH HOH . T 7 HOH B 17 517 48 HOH HOH . T 7 HOH B 18 518 77 HOH HOH . T 7 HOH B 19 519 43 HOH HOH . T 7 HOH B 20 520 65 HOH HOH . T 7 HOH B 21 521 69 HOH HOH . T 7 HOH B 22 522 72 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 PG ATP . . . N 3 211.716 208.346 154.729 1 54.41 ? PG ATP 401 B 1 HETATM 2 O O1G ATP . . . N 3 210.52 207.96 153.896 1 74.47 ? O1G ATP 401 B 1 HETATM 3 O O2G ATP . . . N 3 211.455 209.471 155.696 1 63.24 ? O2G ATP 401 B 1 HETATM 4 O O3G ATP . . . N 3 212.997 208.527 153.948 1 70.72 ? O3G ATP 401 B 1 HETATM 5 P PB ATP . . . N 3 211.396 205.602 155.296 1 57.75 ? PB ATP 401 B 1 HETATM 6 O O1B ATP . . . N 3 211.783 205.256 153.878 1 63.64 ? O1B ATP 401 B 1 HETATM 7 O O2B ATP . . . N 3 209.94 205.574 155.683 1 66.84 ? O2B ATP 401 B 1 HETATM 8 O O3B ATP . . . N 3 211.959 207.065 155.684 1 59.37 ? O3B ATP 401 B 1 HETATM 9 P PA ATP . . . N 3 213.768 204.473 156.489 1 71.46 ? PA ATP 401 B 1 HETATM 10 O O1A ATP . . . N 3 214.49 205.134 155.34 1 67.35 ? O1A ATP 401 B 1 HETATM 11 O O2A ATP . . . N 3 214.071 203.029 156.824 1 64.62 ? O2A ATP 401 B 1 HETATM 12 O O3A ATP . . . N 3 212.163 204.585 156.293 1 85.35 ? O3A ATP 401 B 1 HETATM 13 O O5' ATP . . . N 3 214.022 205.33 157.821 1 55.96 ? O5' ATP 401 B 1 HETATM 14 C C5' ATP . . . N 3 213.452 204.867 159.042 1 63 ? C5' ATP 401 B 1 HETATM 15 C C4' ATP . . . N 3 213.136 206.064 159.912 1 64.88 ? C4' ATP 401 B 1 HETATM 16 O O4' ATP . . . N 3 214.343 206.813 160.099 1 62.24 ? O4' ATP 401 B 1 HETATM 17 C C3' ATP . . . N 3 212.127 206.977 159.234 1 67.04 ? C3' ATP 401 B 1 HETATM 18 O O3' ATP . . . N 3 211.158 207.475 160.166 1 67.86 ? O3' ATP 401 B 1 HETATM 19 C C2' ATP . . . N 3 212.974 208.094 158.67 1 64.64 ? C2' ATP 401 B 1 HETATM 20 O O2' ATP . . . N 3 212.286 209.344 158.618 1 72.3 ? O2' ATP 401 B 1 HETATM 21 C C1' ATP . . . N 3 214.143 208.15 159.64 1 59.4 ? C1' ATP 401 B 1 HETATM 22 N N9 ATP . . . N 3 215.336 208.692 158.961 1 58.18 ? N9 ATP 401 B 1 HETATM 23 C C8 ATP . . . N 3 215.939 208.168 157.879 1 56.74 ? C8 ATP 401 B 1 HETATM 24 N N7 ATP . . . N 3 216.996 208.932 157.518 1 63.37 ? N7 ATP 401 B 1 HETATM 25 C C5 ATP . . . N 3 217.072 209.958 158.379 1 53.28 ? C5 ATP 401 B 1 HETATM 26 C C6 ATP . . . N 3 217.95 211.125 158.563 1 62.54 ? C6 ATP 401 B 1 HETATM 27 N N6 ATP . . . N 3 218.982 211.337 157.726 1 59.06 ? N6 ATP 401 B 1 HETATM 28 N N1 ATP . . . N 3 217.69 211.965 159.587 1 58.13 ? N1 ATP 401 B 1 HETATM 29 C C2 ATP . . . N 3 216.66 211.757 160.422 1 64.05 ? C2 ATP 401 B 1 HETATM 30 N N3 ATP . . . N 3 215.819 210.711 160.309 1 58.95 ? N3 ATP 401 B 1 HETATM 31 C C4 ATP . . . N 3 215.97 209.801 159.325 1 55.16 ? C4 ATP 401 B 1 HETATM 32 H "H5'1" ATP . . . N 3 214.156 204.208 159.555 1 75.6 ? "H5'1" ATP 401 B 1 HETATM 33 H "H5'2" ATP . . . N 3 212.539 204.304 158.837 1 75.6 ? "H5'2" ATP 401 B 1 HETATM 34 H H4' ATP . . . N 3 212.736 205.723 160.878 1 77.85 ? H4' ATP 401 B 1 HETATM 35 H H3' ATP . . . N 3 211.636 206.437 158.412 1 80.45 ? H3' ATP 401 B 1 HETATM 36 H HO3' ATP . . . N 3 210.533 208.051 159.704 1 81.43 ? HO3' ATP 401 B 1 HETATM 37 H H2' ATP . . . N 3 213.338 207.809 157.673 1 77.57 ? H2' ATP 401 B 1 HETATM 38 H HO2' ATP . . . N 3 211.515 209.264 158.04 1 86.76 ? HO2' ATP 401 B 1 HETATM 39 H H1' ATP . . . N 3 213.869 208.797 160.485 1 71.28 ? H1' ATP 401 B 1 HETATM 40 H H8 ATP . . . N 3 215.624 207.266 157.369 1 68.09 ? H8 ATP 401 B 1 HETATM 41 H HN61 ATP . . . N 3 219.583 212.138 157.858 1 70.87 ? HN61 ATP 401 B 1 HETATM 42 H HN62 ATP . . . N 3 219.157 210.693 156.968 1 70.87 ? HN62 ATP 401 B 1 HETATM 43 H H2 ATP . . . N 3 216.497 212.464 161.226 1 76.86 ? H2 ATP 401 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #