data_8CLC # _model_server_result.job_id jckOtAHpJqGtr4LPbH4xvg _model_server_result.datetime_utc '2024-11-16 21:35:20' _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 8clc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":401}' # _entry.id 8CLC # _exptl.entry_id 8CLC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _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 8CLC _cell.length_a 106.53 _cell.length_b 160.48 _cell.length_c 181.24 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CLC _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 PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,S,T,U,V _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 9 _struct_asym.id P _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc8 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc10 H MG MG . A MG 502 1_555 Q O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc11 H MG MG . A MG 502 1_555 Q O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc12 H MG MG . A MG 502 1_555 Q O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc13 J O1A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc14 K MG MG . B MG 502 1_555 R O HOH . B HOH 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc15 C OD1 ASP 39 C ASP 39 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc16 C OD2 ASP 39 C ASP 39 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc17 C O THR 41 C THR 41 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc18 C OG1 THR 41 C THR 41 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc19 C O GLY 44 C GLY 44 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc20 C OE1 GLU 55 C GLU 55 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc21 C OE2 GLU 55 C GLU 55 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc22 L O1G GTP . C GTP 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc23 L O1B GTP . C GTP 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc24 M MG MG . C MG 502 1_555 S O HOH . C HOH 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc25 M MG MG . C MG 502 1_555 S O HOH . C HOH 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc26 M MG MG . C MG 502 1_555 S O HOH . C HOH 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 PG O1G ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 8CLC _atom_sites.fract_transf_matrix[1][1] 0.009387 _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] 0.006231 _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] 0.005518 _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 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 GDP B 1 501 501 GDP GDP . K 6 MG B 1 502 502 MG MG . L 5 GTP C 1 501 501 GTP GTP . M 6 MG C 1 502 502 MG MG . N 7 CA C 1 503 503 CA CA . O 8 GDP D 1 501 501 GDP GDP . P 9 ACP F 1 401 401 ACP ACP . Q 10 HOH A 1 601 111 HOH HOH . Q 10 HOH A 2 602 38 HOH HOH . Q 10 HOH A 3 603 91 HOH HOH . Q 10 HOH A 4 604 97 HOH HOH . Q 10 HOH A 5 605 106 HOH HOH . Q 10 HOH A 6 606 17 HOH HOH . Q 10 HOH A 7 607 85 HOH HOH . Q 10 HOH A 8 608 65 HOH HOH . Q 10 HOH A 9 609 67 HOH HOH . Q 10 HOH A 10 610 110 HOH HOH . Q 10 HOH A 11 611 45 HOH HOH . Q 10 HOH A 12 612 12 HOH HOH . Q 10 HOH A 13 613 8 HOH HOH . Q 10 HOH A 14 614 86 HOH HOH . Q 10 HOH A 15 615 94 HOH HOH . R 10 HOH B 1 601 90 HOH HOH . R 10 HOH B 2 602 15 HOH HOH . R 10 HOH B 3 603 52 HOH HOH . R 10 HOH B 4 604 74 HOH HOH . R 10 HOH B 5 605 11 HOH HOH . R 10 HOH B 6 606 68 HOH HOH . R 10 HOH B 7 607 36 HOH HOH . R 10 HOH B 8 608 72 HOH HOH . R 10 HOH B 9 609 26 HOH HOH . R 10 HOH B 10 610 75 HOH HOH . R 10 HOH B 11 611 107 HOH HOH . R 10 HOH B 12 612 21 HOH HOH . R 10 HOH B 13 613 35 HOH HOH . R 10 HOH B 14 614 4 HOH HOH . R 10 HOH B 15 615 51 HOH HOH . R 10 HOH B 16 616 55 HOH HOH . R 10 HOH B 17 617 29 HOH HOH . R 10 HOH B 18 618 57 HOH HOH . R 10 HOH B 19 619 93 HOH HOH . R 10 HOH B 20 620 10 HOH HOH . R 10 HOH B 21 621 2 HOH HOH . S 10 HOH C 1 601 60 HOH HOH . S 10 HOH C 2 602 113 HOH HOH . S 10 HOH C 3 603 109 HOH HOH . S 10 HOH C 4 604 79 HOH HOH . S 10 HOH C 5 605 105 HOH HOH . S 10 HOH C 6 606 71 HOH HOH . S 10 HOH C 7 607 14 HOH HOH . S 10 HOH C 8 608 7 HOH HOH . S 10 HOH C 9 609 34 HOH HOH . S 10 HOH C 10 610 78 HOH HOH . S 10 HOH C 11 611 6 HOH HOH . S 10 HOH C 12 612 5 HOH HOH . S 10 HOH C 13 613 58 HOH HOH . S 10 HOH C 14 614 47 HOH HOH . S 10 HOH C 15 615 76 HOH HOH . S 10 HOH C 16 616 33 HOH HOH . S 10 HOH C 17 617 62 HOH HOH . S 10 HOH C 18 618 32 HOH HOH . S 10 HOH C 19 619 28 HOH HOH . S 10 HOH C 20 620 70 HOH HOH . S 10 HOH C 21 621 59 HOH HOH . S 10 HOH C 22 622 61 HOH HOH . S 10 HOH C 23 623 9 HOH HOH . S 10 HOH C 24 624 31 HOH HOH . S 10 HOH C 25 625 27 HOH HOH . S 10 HOH C 26 626 116 HOH HOH . S 10 HOH C 27 627 53 HOH HOH . S 10 HOH C 28 628 43 HOH HOH . S 10 HOH C 29 629 22 HOH HOH . S 10 HOH C 30 630 102 HOH HOH . S 10 HOH C 31 631 84 HOH HOH . S 10 HOH C 32 632 1 HOH HOH . S 10 HOH C 33 633 40 HOH HOH . S 10 HOH C 34 634 23 HOH HOH . S 10 HOH C 35 635 50 HOH HOH . S 10 HOH C 36 636 13 HOH HOH . S 10 HOH C 37 637 18 HOH HOH . S 10 HOH C 38 638 30 HOH HOH . T 10 HOH D 1 601 108 HOH HOH . T 10 HOH D 2 602 66 HOH HOH . T 10 HOH D 3 603 73 HOH HOH . U 10 HOH E 1 201 37 HOH HOH . U 10 HOH E 2 202 25 HOH HOH . V 10 HOH F 1 501 115 HOH HOH . V 10 HOH F 2 502 80 HOH HOH . V 10 HOH F 3 503 83 HOH HOH . V 10 HOH F 4 504 101 HOH HOH . V 10 HOH F 5 505 89 HOH HOH . V 10 HOH F 6 506 54 HOH HOH . V 10 HOH F 7 507 20 HOH HOH . V 10 HOH F 8 508 92 HOH HOH . V 10 HOH F 9 509 39 HOH HOH . V 10 HOH F 10 510 69 HOH HOH . V 10 HOH F 11 511 48 HOH HOH . V 10 HOH F 12 512 3 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 ACP . . . P 9 8 51.385 94.863 1 162.89 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . P 9 7.996 51.933 93.465 1 137.08 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . P 9 6.987 50.288 95.038 1 145.13 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . P 9 7.835 52.469 95.891 1 116.74 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . P 9 10.86 51.717 95.865 1 151 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . P 9 11.137 52.833 94.897 1 117.34 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . P 9 12.041 50.878 96.26 1 141.58 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . P 9 9.613 50.625 95.116 1 145.3 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . P 9 10.685 52.96 98.51 1 128.34 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . P 9 12.069 52.466 98.76 1 145.19 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . P 9 10.449 54.43 98.439 1 101.72 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . P 9 10.147 52.288 97.163 1 134.12 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . P 9 9.688 52.309 99.579 1 125.07 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . P 9 9.346 50.909 99.444 1 127.36 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . P 9 8.469 50.509 100.602 1 115.35 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . P 9 9.169 50.793 101.837 1 115.04 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . P 9 7.138 51.258 100.72 1 115.52 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . P 9 6.115 50.588 99.996 1 110.71 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . P 9 6.875 51.226 102.225 1 116.66 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . P 9 6.247 50.031 102.633 1 116.22 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . P 9 8.284 51.319 102.801 1 114.39 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . P 9 8.712 52.674 103.126 1 111.27 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . P 9 9.492 53.496 102.353 1 112.23 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . P 9 9.734 54.656 102.908 1 107.38 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . P 9 9.08 54.596 104.129 1 109.02 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . P 9 8.96 55.52 105.184 1 105.33 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . P 9 9.513 56.729 105.175 1 92.5 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . P 9 8.236 55.145 106.264 1 100.92 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . P 9 7.679 53.928 106.266 1 107.25 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . P 9 7.726 52.978 105.336 1 111.3 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . P 9 8.45 53.376 104.278 1 111.31 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #